Starting phenix.real_space_refine on Thu Nov 20 04:11:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bqr_7132/11_2025/6bqr_7132.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bqr_7132/11_2025/6bqr_7132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6bqr_7132/11_2025/6bqr_7132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bqr_7132/11_2025/6bqr_7132.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bqr_7132/11_2025/6bqr_7132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bqr_7132/11_2025/6bqr_7132.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 19492 2.51 5 N 5240 2.21 5 O 5228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30116 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7424 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 38, 'TRANS': 909} Chain breaks: 7 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 7424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7424 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 38, 'TRANS': 909} Chain breaks: 7 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 7424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7424 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 38, 'TRANS': 909} Chain breaks: 7 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 7424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7424 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 38, 'TRANS': 909} Chain breaks: 7 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 8, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.43, per 1000 atoms: 0.25 Number of scatterers: 30116 At special positions: 0 Unit cell: (144.348, 145.394, 158.992, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 5228 8.00 N 5240 7.00 C 19492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.05 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1011 " distance=2.05 Simple disulfide: pdb=" SG CYS C 993 " - pdb=" SG CYS C1011 " distance=2.05 Simple disulfide: pdb=" SG CYS D 993 " - pdb=" SG CYS D1011 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.5 seconds 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6992 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 12 sheets defined 66.2% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR A 103 " --> pdb=" O PRO A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.723A pdb=" N ALA A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 removed outlier: 4.430A pdb=" N ARG A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.602A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 4.017A pdb=" N THR A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 4.628A pdb=" N ARG A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.687A pdb=" N LEU A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.588A pdb=" N LEU A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 removed outlier: 3.764A pdb=" N VAL A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.612A pdb=" N ALA A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 483 removed outlier: 3.636A pdb=" N HIS A 482 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 559 through 569 Processing helix chain 'A' and resid 571 through 582 removed outlier: 3.534A pdb=" N MET A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 603 removed outlier: 3.694A pdb=" N ARG A 597 " --> pdb=" O CYS A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 632 removed outlier: 3.672A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.677A pdb=" N LEU A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.574A pdb=" N PHE A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 681 Processing helix chain 'A' and resid 690 through 698 Processing helix chain 'A' and resid 699 through 704 Processing helix chain 'A' and resid 767 through 777 removed outlier: 3.733A pdb=" N ARG A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP A 772 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS A 774 " --> pdb=" O ARG A 770 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 775 " --> pdb=" O ARG A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 803 removed outlier: 3.739A pdb=" N TYR A 790 " --> pdb=" O ASN A 786 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 803 " --> pdb=" O ARG A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 835 removed outlier: 3.689A pdb=" N THR A 823 " --> pdb=" O PHE A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 860 removed outlier: 3.745A pdb=" N ARG A 857 " --> pdb=" O SER A 853 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 858 " --> pdb=" O GLN A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 884 removed outlier: 3.699A pdb=" N THR A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 910 removed outlier: 3.583A pdb=" N MET A 900 " --> pdb=" O CYS A 896 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 923 removed outlier: 3.513A pdb=" N ILE A 922 " --> pdb=" O PRO A 918 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 923 " --> pdb=" O LYS A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 952 Processing helix chain 'A' and resid 958 through 967 removed outlier: 3.618A pdb=" N ARG A 964 " --> pdb=" O PRO A 960 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 967 " --> pdb=" O LEU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 973 removed outlier: 3.643A pdb=" N GLN A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' Processing helix chain 'A' and resid 979 through 984 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 1016 through 1031 removed outlier: 3.532A pdb=" N VAL A1021 " --> pdb=" O ASN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1072 removed outlier: 3.838A pdb=" N GLN A1051 " --> pdb=" O PHE A1047 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A1056 " --> pdb=" O GLY A1052 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS A1070 " --> pdb=" O ILE A1066 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A1071 " --> pdb=" O ARG A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1089 removed outlier: 3.503A pdb=" N ARG A1086 " --> pdb=" O ILE A1082 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A1087 " --> pdb=" O SER A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1142 removed outlier: 4.278A pdb=" N ARG A1119 " --> pdb=" O LYS A1115 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A1120 " --> pdb=" O GLU A1116 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG A1138 " --> pdb=" O LEU A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1164 removed outlier: 3.848A pdb=" N LEU A1157 " --> pdb=" O GLN A1153 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A1164 " --> pdb=" O LYS A1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.805A pdb=" N TYR B 103 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.723A pdb=" N ALA B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 260 removed outlier: 4.430A pdb=" N ARG B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.602A pdb=" N LEU B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 removed outlier: 4.017A pdb=" N THR B 314 " --> pdb=" O CYS B 310 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 4.628A pdb=" N ARG B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 358 removed outlier: 3.687A pdb=" N LEU B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 removed outlier: 3.588A pdb=" N LEU B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 removed outlier: 3.764A pdb=" N VAL B 441 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.611A pdb=" N ALA B 466 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 483 removed outlier: 3.637A pdb=" N HIS B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 559 through 569 Processing helix chain 'B' and resid 571 through 582 removed outlier: 3.533A pdb=" N MET B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 603 removed outlier: 3.695A pdb=" N ARG B 597 " --> pdb=" O CYS B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 632 removed outlier: 3.673A pdb=" N ALA B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 removed outlier: 3.677A pdb=" N LEU B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 663 through 669 removed outlier: 3.575A pdb=" N PHE B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN B 669 " --> pdb=" O ALA B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 681 Processing helix chain 'B' and resid 690 through 698 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 767 through 777 removed outlier: 3.733A pdb=" N ARG B 771 " --> pdb=" O ARG B 767 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP B 772 " --> pdb=" O CYS B 768 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS B 774 " --> pdb=" O ARG B 770 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 803 removed outlier: 3.739A pdb=" N TYR B 790 " --> pdb=" O ASN B 786 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 803 " --> pdb=" O ARG B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 835 removed outlier: 3.689A pdb=" N THR B 823 " --> pdb=" O PHE B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 860 removed outlier: 3.745A pdb=" N ARG B 857 " --> pdb=" O SER B 853 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 858 " --> pdb=" O GLN B 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 884 removed outlier: 3.699A pdb=" N THR B 884 " --> pdb=" O GLY B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 910 removed outlier: 3.583A pdb=" N MET B 900 " --> pdb=" O CYS B 896 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU B 907 " --> pdb=" O THR B 903 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 926 removed outlier: 3.514A pdb=" N ILE B 922 " --> pdb=" O PRO B 918 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 923 " --> pdb=" O LYS B 919 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS B 925 " --> pdb=" O VAL B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 952 Processing helix chain 'B' and resid 958 through 967 removed outlier: 3.617A pdb=" N ARG B 964 " --> pdb=" O PRO B 960 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 967 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 973 removed outlier: 3.642A pdb=" N GLN B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 976 No H-bonds generated for 'chain 'B' and resid 974 through 976' Processing helix chain 'B' and resid 979 through 984 Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 1016 through 1031 removed outlier: 3.532A pdb=" N VAL B1021 " --> pdb=" O ASN B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1072 removed outlier: 3.838A pdb=" N GLN B1051 " --> pdb=" O PHE B1047 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B1056 " --> pdb=" O GLY B1052 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA B1060 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS B1070 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B1071 " --> pdb=" O ARG B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1089 removed outlier: 3.503A pdb=" N ARG B1086 " --> pdb=" O ILE B1082 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B1087 " --> pdb=" O SER B1083 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1142 removed outlier: 4.278A pdb=" N ARG B1119 " --> pdb=" O LYS B1115 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS B1120 " --> pdb=" O GLU B1116 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1164 removed outlier: 3.848A pdb=" N LEU B1157 " --> pdb=" O GLN B1153 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS B1164 " --> pdb=" O LYS B1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 141 through 150 removed outlier: 3.723A pdb=" N ALA C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C 149 " --> pdb=" O ALA C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 260 removed outlier: 4.430A pdb=" N ARG C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.601A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN C 290 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 removed outlier: 4.017A pdb=" N THR C 314 " --> pdb=" O CYS C 310 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 4.628A pdb=" N ARG C 332 " --> pdb=" O GLN C 328 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP C 333 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 358 removed outlier: 3.687A pdb=" N LEU C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU C 381 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 403 Processing helix chain 'C' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 removed outlier: 3.588A pdb=" N LEU C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 431 " --> pdb=" O ALA C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 removed outlier: 3.763A pdb=" N VAL C 441 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 removed outlier: 3.613A pdb=" N ALA C 466 " --> pdb=" O GLN C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 483 removed outlier: 3.637A pdb=" N HIS C 482 " --> pdb=" O ASP C 478 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER C 483 " --> pdb=" O GLN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 510 Processing helix chain 'C' and resid 559 through 569 Processing helix chain 'C' and resid 571 through 582 removed outlier: 3.534A pdb=" N MET C 576 " --> pdb=" O ALA C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 603 removed outlier: 3.695A pdb=" N ARG C 597 " --> pdb=" O CYS C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 632 removed outlier: 3.672A pdb=" N ALA C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 619 " --> pdb=" O LEU C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.677A pdb=" N LEU C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 661 Processing helix chain 'C' and resid 663 through 669 removed outlier: 3.574A pdb=" N PHE C 667 " --> pdb=" O ALA C 663 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 681 Processing helix chain 'C' and resid 690 through 698 Processing helix chain 'C' and resid 699 through 704 Processing helix chain 'C' and resid 767 through 777 removed outlier: 3.732A pdb=" N ARG C 771 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP C 772 " --> pdb=" O CYS C 768 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS C 774 " --> pdb=" O ARG C 770 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 775 " --> pdb=" O ARG C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 803 removed outlier: 3.739A pdb=" N TYR C 790 " --> pdb=" O ASN C 786 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 803 " --> pdb=" O ARG C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 835 removed outlier: 3.689A pdb=" N THR C 823 " --> pdb=" O PHE C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 860 removed outlier: 3.745A pdb=" N ARG C 857 " --> pdb=" O SER C 853 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 858 " --> pdb=" O GLN C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 884 removed outlier: 3.699A pdb=" N THR C 884 " --> pdb=" O GLY C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 910 removed outlier: 3.584A pdb=" N MET C 900 " --> pdb=" O CYS C 896 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 907 " --> pdb=" O THR C 903 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 923 removed outlier: 3.513A pdb=" N ILE C 922 " --> pdb=" O PRO C 918 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 923 " --> pdb=" O LYS C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 952 Processing helix chain 'C' and resid 958 through 967 removed outlier: 3.618A pdb=" N ARG C 964 " --> pdb=" O PRO C 960 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 967 " --> pdb=" O LEU C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 973 removed outlier: 3.642A pdb=" N GLN C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 976 No H-bonds generated for 'chain 'C' and resid 974 through 976' Processing helix chain 'C' and resid 979 through 984 Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 1016 through 1031 removed outlier: 3.532A pdb=" N VAL C1021 " --> pdb=" O ASN C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1072 removed outlier: 3.839A pdb=" N GLN C1051 " --> pdb=" O PHE C1047 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C1056 " --> pdb=" O GLY C1052 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA C1060 " --> pdb=" O LEU C1056 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS C1070 " --> pdb=" O ILE C1066 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER C1071 " --> pdb=" O ARG C1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 1080 through 1089 removed outlier: 3.502A pdb=" N ARG C1086 " --> pdb=" O ILE C1082 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C1087 " --> pdb=" O SER C1083 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1142 removed outlier: 4.279A pdb=" N ARG C1119 " --> pdb=" O LYS C1115 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C1120 " --> pdb=" O GLU C1116 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG C1138 " --> pdb=" O LEU C1134 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1164 removed outlier: 3.849A pdb=" N LEU C1157 " --> pdb=" O GLN C1153 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS C1164 " --> pdb=" O LYS C1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR D 103 " --> pdb=" O PRO D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 141 through 150 removed outlier: 3.723A pdb=" N ALA D 145 " --> pdb=" O GLY D 141 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 260 removed outlier: 4.431A pdb=" N ARG D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.602A pdb=" N LEU D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 removed outlier: 4.016A pdb=" N THR D 314 " --> pdb=" O CYS D 310 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 316 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 4.629A pdb=" N ARG D 332 " --> pdb=" O GLN D 328 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP D 333 " --> pdb=" O GLY D 329 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 335 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 358 removed outlier: 3.687A pdb=" N LEU D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 353 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU D 381 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.748A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 removed outlier: 3.588A pdb=" N LEU D 425 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 removed outlier: 3.765A pdb=" N VAL D 441 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 466 removed outlier: 3.612A pdb=" N ALA D 466 " --> pdb=" O GLN D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.636A pdb=" N HIS D 482 " --> pdb=" O ASP D 478 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER D 483 " --> pdb=" O GLN D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 510 Processing helix chain 'D' and resid 559 through 569 Processing helix chain 'D' and resid 571 through 582 removed outlier: 3.534A pdb=" N MET D 576 " --> pdb=" O ALA D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 603 removed outlier: 3.694A pdb=" N ARG D 597 " --> pdb=" O CYS D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 632 removed outlier: 3.673A pdb=" N ALA D 609 " --> pdb=" O ASP D 605 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE D 619 " --> pdb=" O LEU D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 removed outlier: 3.678A pdb=" N LEU D 642 " --> pdb=" O ALA D 638 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 661 Processing helix chain 'D' and resid 663 through 669 removed outlier: 3.574A pdb=" N PHE D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 681 Processing helix chain 'D' and resid 690 through 698 Processing helix chain 'D' and resid 699 through 704 Processing helix chain 'D' and resid 767 through 777 removed outlier: 3.733A pdb=" N ARG D 771 " --> pdb=" O ARG D 767 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP D 772 " --> pdb=" O CYS D 768 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS D 774 " --> pdb=" O ARG D 770 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 775 " --> pdb=" O ARG D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 803 removed outlier: 3.739A pdb=" N TYR D 790 " --> pdb=" O ASN D 786 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 835 removed outlier: 3.689A pdb=" N THR D 823 " --> pdb=" O PHE D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 860 removed outlier: 3.745A pdb=" N ARG D 857 " --> pdb=" O SER D 853 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU D 858 " --> pdb=" O GLN D 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 884 removed outlier: 3.699A pdb=" N THR D 884 " --> pdb=" O GLY D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 910 removed outlier: 3.583A pdb=" N MET D 900 " --> pdb=" O CYS D 896 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 907 " --> pdb=" O THR D 903 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS D 908 " --> pdb=" O VAL D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 926 removed outlier: 3.513A pdb=" N ILE D 922 " --> pdb=" O PRO D 918 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 923 " --> pdb=" O LYS D 919 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS D 925 " --> pdb=" O VAL D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 952 Processing helix chain 'D' and resid 958 through 967 removed outlier: 3.618A pdb=" N ARG D 964 " --> pdb=" O PRO D 960 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 967 " --> pdb=" O LEU D 963 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 973 removed outlier: 3.643A pdb=" N GLN D 973 " --> pdb=" O ARG D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 974 through 976 No H-bonds generated for 'chain 'D' and resid 974 through 976' Processing helix chain 'D' and resid 979 through 984 Processing helix chain 'D' and resid 985 through 988 Processing helix chain 'D' and resid 1016 through 1031 removed outlier: 3.531A pdb=" N VAL D1021 " --> pdb=" O ASN D1017 " (cutoff:3.500A) Processing helix chain 'D' and resid 1034 through 1072 removed outlier: 3.838A pdb=" N GLN D1051 " --> pdb=" O PHE D1047 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D1056 " --> pdb=" O GLY D1052 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA D1060 " --> pdb=" O LEU D1056 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS D1070 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER D1071 " --> pdb=" O ARG D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1080 through 1089 removed outlier: 3.503A pdb=" N ARG D1086 " --> pdb=" O ILE D1082 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU D1087 " --> pdb=" O SER D1083 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1142 removed outlier: 4.279A pdb=" N ARG D1119 " --> pdb=" O LYS D1115 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS D1120 " --> pdb=" O GLU D1116 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG D1138 " --> pdb=" O LEU D1134 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1164 removed outlier: 3.848A pdb=" N LEU D1157 " --> pdb=" O GLN D1153 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS D1164 " --> pdb=" O LYS D1160 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 93 removed outlier: 6.933A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 187 removed outlier: 3.582A pdb=" N VAL A 119 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 262 Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 93 removed outlier: 6.933A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.582A pdb=" N VAL B 119 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 118 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU B 276 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER B 120 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 261 through 262 Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 93 removed outlier: 6.932A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 185 through 187 removed outlier: 3.582A pdb=" N VAL C 119 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL C 118 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU C 276 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER C 120 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 261 through 262 Processing sheet with id=AB1, first strand: chain 'D' and resid 89 through 93 removed outlier: 6.932A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 185 through 187 removed outlier: 3.583A pdb=" N VAL D 119 " --> pdb=" O TRP D 152 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL D 118 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU D 276 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER D 120 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 261 through 262 1510 hydrogen bonds defined for protein. 4470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.71 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4734 1.31 - 1.44: 8427 1.44 - 1.56: 17262 1.56 - 1.69: 145 1.69 - 1.82: 252 Bond restraints: 30820 Sorted by residual: bond pdb=" CAI Y01 B1302 " pdb=" CAZ Y01 B1302 " ideal model delta sigma weight residual 1.332 1.677 -0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" CAI Y01 C1302 " pdb=" CAZ Y01 C1302 " ideal model delta sigma weight residual 1.332 1.677 -0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" CAI Y01 D1302 " pdb=" CAZ Y01 D1302 " ideal model delta sigma weight residual 1.332 1.677 -0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" CAI Y01 A1302 " pdb=" CAZ Y01 A1302 " ideal model delta sigma weight residual 1.332 1.676 -0.344 2.00e-02 2.50e+03 2.96e+02 bond pdb=" CAI Y01 C1301 " pdb=" CAZ Y01 C1301 " ideal model delta sigma weight residual 1.332 1.674 -0.342 2.00e-02 2.50e+03 2.93e+02 ... (remaining 30815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 39801 2.51 - 5.02: 1566 5.02 - 7.53: 338 7.53 - 10.03: 107 10.03 - 12.54: 24 Bond angle restraints: 41836 Sorted by residual: angle pdb=" N ILE B1165 " pdb=" CA ILE B1165 " pdb=" C ILE B1165 " ideal model delta sigma weight residual 113.10 108.06 5.04 9.70e-01 1.06e+00 2.70e+01 angle pdb=" N ILE A1165 " pdb=" CA ILE A1165 " pdb=" C ILE A1165 " ideal model delta sigma weight residual 113.10 108.08 5.02 9.70e-01 1.06e+00 2.68e+01 angle pdb=" N ILE D1165 " pdb=" CA ILE D1165 " pdb=" C ILE D1165 " ideal model delta sigma weight residual 113.10 108.08 5.02 9.70e-01 1.06e+00 2.67e+01 angle pdb=" N ILE C1165 " pdb=" CA ILE C1165 " pdb=" C ILE C1165 " ideal model delta sigma weight residual 113.10 108.09 5.01 9.70e-01 1.06e+00 2.67e+01 angle pdb=" CA TRP B 152 " pdb=" CB TRP B 152 " pdb=" CG TRP B 152 " ideal model delta sigma weight residual 113.60 123.16 -9.56 1.90e+00 2.77e-01 2.53e+01 ... (remaining 41831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 17036 16.00 - 32.01: 1282 32.01 - 48.01: 398 48.01 - 64.01: 40 64.01 - 80.02: 32 Dihedral angle restraints: 18788 sinusoidal: 7940 harmonic: 10848 Sorted by residual: dihedral pdb=" CA ALA A 392 " pdb=" C ALA A 392 " pdb=" N TYR A 393 " pdb=" CA TYR A 393 " ideal model delta harmonic sigma weight residual 180.00 -145.46 -34.54 0 5.00e+00 4.00e-02 4.77e+01 dihedral pdb=" CA ALA C 392 " pdb=" C ALA C 392 " pdb=" N TYR C 393 " pdb=" CA TYR C 393 " ideal model delta harmonic sigma weight residual -180.00 -145.46 -34.54 0 5.00e+00 4.00e-02 4.77e+01 dihedral pdb=" CA ALA D 392 " pdb=" C ALA D 392 " pdb=" N TYR D 393 " pdb=" CA TYR D 393 " ideal model delta harmonic sigma weight residual 180.00 -145.48 -34.52 0 5.00e+00 4.00e-02 4.77e+01 ... (remaining 18785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 4514 0.118 - 0.237: 166 0.237 - 0.355: 20 0.355 - 0.474: 12 0.474 - 0.592: 4 Chirality restraints: 4716 Sorted by residual: chirality pdb=" CBI Y01 C1303 " pdb=" CAU Y01 C1303 " pdb=" CBE Y01 C1303 " pdb=" CBG Y01 C1303 " both_signs ideal model delta sigma weight residual False 2.94 2.34 0.59 2.00e-01 2.50e+01 8.76e+00 chirality pdb=" CBI Y01 B1303 " pdb=" CAU Y01 B1303 " pdb=" CBE Y01 B1303 " pdb=" CBG Y01 B1303 " both_signs ideal model delta sigma weight residual False 2.94 2.35 0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" CBI Y01 D1303 " pdb=" CAU Y01 D1303 " pdb=" CBE Y01 D1303 " pdb=" CBG Y01 D1303 " both_signs ideal model delta sigma weight residual False 2.94 2.35 0.59 2.00e-01 2.50e+01 8.68e+00 ... (remaining 4713 not shown) Planarity restraints: 5252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 152 " -0.043 2.00e-02 2.50e+03 2.84e-02 2.01e+01 pdb=" CG TRP B 152 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP B 152 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 152 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 152 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 152 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 152 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 152 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 152 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 152 " 0.043 2.00e-02 2.50e+03 2.83e-02 2.01e+01 pdb=" CG TRP D 152 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP D 152 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 152 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP D 152 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 152 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 152 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 152 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 152 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 152 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 152 " -0.043 2.00e-02 2.50e+03 2.83e-02 2.01e+01 pdb=" CG TRP A 152 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP A 152 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 152 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 152 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 152 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 152 " -0.009 2.00e-02 2.50e+03 ... (remaining 5249 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 30 2.03 - 2.75: 4170 2.75 - 3.47: 43176 3.47 - 4.18: 73164 4.18 - 4.90: 125484 Nonbonded interactions: 246024 Sorted by model distance: nonbonded pdb=" CB TYR B 211 " pdb=" OH TYR B 227 " model vdw 1.313 3.440 nonbonded pdb=" CB TYR C 211 " pdb=" OH TYR C 227 " model vdw 1.313 3.440 nonbonded pdb=" CB TYR D 211 " pdb=" OH TYR D 227 " model vdw 1.314 3.440 nonbonded pdb=" CB TYR A 211 " pdb=" OH TYR A 227 " model vdw 1.314 3.440 nonbonded pdb=" O GLY C 157 " pdb=" OD1 ASP C 226 " model vdw 1.532 3.040 ... (remaining 246019 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 28.760 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.345 30824 Z= 0.588 Angle : 1.264 12.542 41844 Z= 0.658 Chirality : 0.065 0.592 4716 Planarity : 0.008 0.075 5252 Dihedral : 12.990 80.015 11784 Min Nonbonded Distance : 1.313 Molprobity Statistics. All-atom Clashscore : 26.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.66 % Favored : 90.13 % Rotamer: Outliers : 2.07 % Allowed : 8.42 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.81 (0.09), residues: 3728 helix: -3.71 (0.06), residues: 2352 sheet: -4.91 (0.20), residues: 216 loop : -3.39 (0.16), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 287 TYR 0.022 0.003 TYR A1063 PHE 0.030 0.003 PHE B 90 TRP 0.074 0.005 TRP A 152 HIS 0.008 0.001 HIS B 447 Details of bonding type rmsd covalent geometry : bond 0.01207 (30820) covalent geometry : angle 1.26393 (41836) SS BOND : bond 0.01680 ( 4) SS BOND : angle 2.00778 ( 8) hydrogen bonds : bond 0.28335 ( 1510) hydrogen bonds : angle 10.10822 ( 4470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1110 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 GLN cc_start: 0.6846 (mt0) cc_final: 0.6434 (mp10) REVERT: A 172 ASP cc_start: 0.8148 (m-30) cc_final: 0.7766 (t0) REVERT: A 173 HIS cc_start: 0.8686 (t-90) cc_final: 0.8317 (t-170) REVERT: A 281 ASP cc_start: 0.7596 (m-30) cc_final: 0.7279 (p0) REVERT: A 284 MET cc_start: 0.6060 (tpp) cc_final: 0.5686 (tpp) REVERT: A 376 ILE cc_start: 0.9370 (mt) cc_final: 0.8960 (mt) REVERT: A 398 ARG cc_start: 0.7634 (ttt180) cc_final: 0.7431 (ttt180) REVERT: A 426 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7288 (tt0) REVERT: A 454 PHE cc_start: 0.8432 (t80) cc_final: 0.7823 (t80) REVERT: A 459 ARG cc_start: 0.8657 (mtp85) cc_final: 0.7571 (mtp85) REVERT: A 509 MET cc_start: 0.6856 (ttt) cc_final: 0.6314 (mmp) REVERT: A 577 TYR cc_start: 0.8558 (t80) cc_final: 0.8348 (t80) REVERT: A 590 LEU cc_start: 0.9352 (mm) cc_final: 0.9067 (mm) REVERT: A 615 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8772 (tp) REVERT: A 679 LYS cc_start: 0.9214 (mmpt) cc_final: 0.9009 (mmtm) REVERT: A 800 VAL cc_start: 0.9009 (p) cc_final: 0.8671 (p) REVERT: A 813 LEU cc_start: 0.8922 (mt) cc_final: 0.8606 (mt) REVERT: A 814 GLU cc_start: 0.7618 (tp30) cc_final: 0.7388 (tp30) REVERT: A 831 GLN cc_start: 0.8371 (tt0) cc_final: 0.8161 (tt0) REVERT: A 1044 SER cc_start: 0.8788 (m) cc_final: 0.8588 (m) REVERT: A 1129 LYS cc_start: 0.8756 (ttpt) cc_final: 0.7860 (ptmm) REVERT: A 1140 LYS cc_start: 0.9157 (ttmm) cc_final: 0.8867 (tptp) REVERT: A 1161 GLN cc_start: 0.9084 (mm110) cc_final: 0.8549 (mt0) REVERT: B 420 TRP cc_start: 0.5789 (m100) cc_final: 0.5327 (m100) REVERT: B 426 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7119 (tp30) REVERT: B 454 PHE cc_start: 0.8299 (t80) cc_final: 0.8093 (t80) REVERT: B 459 ARG cc_start: 0.8649 (mtp85) cc_final: 0.7875 (mtp180) REVERT: B 505 HIS cc_start: 0.6667 (t70) cc_final: 0.6442 (t-170) REVERT: B 608 GLU cc_start: 0.7942 (tp30) cc_final: 0.7414 (tp30) REVERT: B 622 MET cc_start: 0.8392 (ttp) cc_final: 0.8127 (ttp) REVERT: B 625 ASP cc_start: 0.8360 (m-30) cc_final: 0.8022 (m-30) REVERT: B 865 ASN cc_start: 0.8571 (m-40) cc_final: 0.8364 (m-40) REVERT: B 879 VAL cc_start: 0.8966 (t) cc_final: 0.8736 (t) REVERT: B 980 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8103 (mt0) REVERT: B 1015 TYR cc_start: 0.8618 (t80) cc_final: 0.8375 (t80) REVERT: B 1129 LYS cc_start: 0.8460 (ttpt) cc_final: 0.8120 (ttpt) REVERT: B 1140 LYS cc_start: 0.9062 (ttmm) cc_final: 0.8531 (ttmm) REVERT: B 1160 LYS cc_start: 0.8996 (mmtp) cc_final: 0.7973 (tptp) REVERT: C 155 THR cc_start: 0.7707 (p) cc_final: 0.7308 (t) REVERT: C 355 MET cc_start: 0.5240 (tpp) cc_final: 0.4984 (tpt) REVERT: C 383 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7344 (tttm) REVERT: C 420 TRP cc_start: 0.5860 (m100) cc_final: 0.5309 (m100) REVERT: C 426 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7029 (tp30) REVERT: C 454 PHE cc_start: 0.8364 (t80) cc_final: 0.7769 (t80) REVERT: C 509 MET cc_start: 0.6574 (ttt) cc_final: 0.6027 (mmp) REVERT: C 578 PHE cc_start: 0.9123 (m-10) cc_final: 0.8716 (m-80) REVERT: C 601 ARG cc_start: 0.8241 (mtp-110) cc_final: 0.7861 (mtt180) REVERT: C 625 ASP cc_start: 0.8348 (m-30) cc_final: 0.8118 (m-30) REVERT: C 626 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9293 (tp) REVERT: C 804 ASP cc_start: 0.7065 (t0) cc_final: 0.6645 (t0) REVERT: C 879 VAL cc_start: 0.8944 (t) cc_final: 0.8553 (t) REVERT: C 1067 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7876 (ttt90) REVERT: C 1125 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8350 (tm-30) REVERT: C 1140 LYS cc_start: 0.9136 (ttmm) cc_final: 0.8658 (ttmm) REVERT: C 1160 LYS cc_start: 0.8922 (mmtp) cc_final: 0.8479 (mmtp) REVERT: D 355 MET cc_start: 0.4820 (tpp) cc_final: 0.4585 (tpt) REVERT: D 383 LYS cc_start: 0.7640 (mtpt) cc_final: 0.7277 (tttm) REVERT: D 420 TRP cc_start: 0.5816 (m100) cc_final: 0.5200 (m100) REVERT: D 426 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6923 (tp30) REVERT: D 454 PHE cc_start: 0.8244 (t80) cc_final: 0.6939 (t80) REVERT: D 459 ARG cc_start: 0.8479 (mtp85) cc_final: 0.7060 (mtp85) REVERT: D 509 MET cc_start: 0.6483 (ttt) cc_final: 0.5897 (mmp) REVERT: D 578 PHE cc_start: 0.9077 (m-10) cc_final: 0.8839 (m-80) REVERT: D 601 ARG cc_start: 0.8174 (mtp-110) cc_final: 0.7898 (mtt180) REVERT: D 608 GLU cc_start: 0.7749 (tp30) cc_final: 0.7542 (tp30) REVERT: D 625 ASP cc_start: 0.8294 (m-30) cc_final: 0.7913 (m-30) REVERT: D 804 ASP cc_start: 0.7083 (t0) cc_final: 0.6655 (t0) REVERT: D 879 VAL cc_start: 0.8944 (t) cc_final: 0.8553 (t) REVERT: D 892 ARG cc_start: 0.8167 (ttt180) cc_final: 0.7746 (ttt-90) REVERT: D 980 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: D 1015 TYR cc_start: 0.8680 (t80) cc_final: 0.8441 (t80) REVERT: D 1045 TYR cc_start: 0.8345 (t80) cc_final: 0.8089 (t80) REVERT: D 1067 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7852 (ttt90) REVERT: D 1125 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8247 (tm-30) REVERT: D 1129 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8008 (ttmt) REVERT: D 1140 LYS cc_start: 0.9091 (ttmm) cc_final: 0.8683 (ttmm) REVERT: D 1160 LYS cc_start: 0.8925 (mmtp) cc_final: 0.8156 (mmtp) outliers start: 64 outliers final: 16 residues processed: 1152 average time/residue: 0.2304 time to fit residues: 402.0766 Evaluate side-chains 764 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 744 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 914 LYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 914 LYS Chi-restraints excluded: chain B residue 980 GLN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 914 LYS Chi-restraints excluded: chain C residue 980 GLN Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 914 LYS Chi-restraints excluded: chain D residue 980 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 173 HIS A 228 ASN A 348 GLN A 404 ASN A 570 ASN A 673 GLN A 774 HIS A 786 ASN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN A1153 GLN A1161 GLN B 116 ASN B 174 GLN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 GLN B 348 GLN B 447 HIS B 462 GLN B 570 ASN B 660 GLN B 673 GLN B 774 HIS B 786 ASN B 889 HIS B1037 ASN B1070 HIS ** B1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1131 ASN C 116 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 GLN C 228 ASN C 462 GLN C 660 GLN C 673 GLN C 774 HIS C 786 ASN ** C1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN C1108 HIS C1131 ASN D 116 ASN D 147 GLN D 165 HIS ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 348 GLN D 462 GLN D 570 ASN D 660 GLN D 774 HIS D 786 ASN D1037 ASN D1108 HIS D1131 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.183343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133141 restraints weight = 47184.084| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.66 r_work: 0.3424 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30824 Z= 0.162 Angle : 0.761 9.764 41844 Z= 0.374 Chirality : 0.042 0.202 4716 Planarity : 0.006 0.069 5252 Dihedral : 8.133 89.576 5047 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.47 % Allowed : 16.48 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.12), residues: 3728 helix: -1.55 (0.09), residues: 2404 sheet: -4.57 (0.22), residues: 192 loop : -3.22 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 611 TYR 0.020 0.002 TYR D 888 PHE 0.022 0.002 PHE D 899 TRP 0.025 0.002 TRP C 820 HIS 0.011 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00370 (30820) covalent geometry : angle 0.76117 (41836) SS BOND : bond 0.00084 ( 4) SS BOND : angle 0.51404 ( 8) hydrogen bonds : bond 0.04345 ( 1510) hydrogen bonds : angle 4.92921 ( 4470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 893 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7112 (tt) REVERT: A 173 HIS cc_start: 0.8704 (t70) cc_final: 0.8411 (t70) REVERT: A 186 MET cc_start: 0.8081 (mpt) cc_final: 0.7858 (mpt) REVERT: A 281 ASP cc_start: 0.8069 (m-30) cc_final: 0.7383 (p0) REVERT: A 284 MET cc_start: 0.5986 (tpp) cc_final: 0.5517 (ttp) REVERT: A 413 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8436 (mt) REVERT: A 454 PHE cc_start: 0.7966 (t80) cc_final: 0.7730 (t80) REVERT: A 462 GLN cc_start: 0.8917 (mt0) cc_final: 0.8672 (mt0) REVERT: A 509 MET cc_start: 0.6621 (ttt) cc_final: 0.5965 (mmp) REVERT: A 601 ARG cc_start: 0.8639 (mtp-110) cc_final: 0.8408 (ptm160) REVERT: A 629 GLU cc_start: 0.8763 (tt0) cc_final: 0.8411 (tt0) REVERT: A 656 GLN cc_start: 0.8581 (mt0) cc_final: 0.8181 (mt0) REVERT: A 660 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8135 (mp-120) REVERT: A 694 VAL cc_start: 0.9407 (t) cc_final: 0.9180 (m) REVERT: A 786 ASN cc_start: 0.9077 (m-40) cc_final: 0.8839 (m-40) REVERT: A 804 ASP cc_start: 0.7530 (t0) cc_final: 0.7293 (t0) REVERT: A 827 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7968 (mm-30) REVERT: A 857 ARG cc_start: 0.7185 (ttm110) cc_final: 0.6790 (ptp-110) REVERT: A 866 GLN cc_start: 0.8492 (mt0) cc_final: 0.8283 (mt0) REVERT: A 1029 LEU cc_start: 0.9456 (tp) cc_final: 0.9122 (tp) REVERT: A 1067 ARG cc_start: 0.8593 (tmm-80) cc_final: 0.7891 (ttt90) REVERT: A 1080 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7576 (tt) REVERT: A 1138 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8207 (ttm110) REVERT: A 1161 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8686 (mt0) REVERT: B 316 GLU cc_start: 0.7862 (mp0) cc_final: 0.7657 (mp0) REVERT: B 372 GLU cc_start: 0.8444 (mp0) cc_final: 0.8202 (pm20) REVERT: B 459 ARG cc_start: 0.7702 (mtp85) cc_final: 0.7449 (mtp180) REVERT: B 584 ASN cc_start: 0.8786 (m-40) cc_final: 0.8549 (m-40) REVERT: B 595 LEU cc_start: 0.9203 (mp) cc_final: 0.8947 (mp) REVERT: B 601 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7537 (mtt180) REVERT: B 629 GLU cc_start: 0.8721 (tt0) cc_final: 0.8207 (tt0) REVERT: B 710 PHE cc_start: 0.8608 (m-80) cc_final: 0.8352 (m-80) REVERT: B 828 GLU cc_start: 0.8165 (tp30) cc_final: 0.7442 (tm-30) REVERT: B 865 ASN cc_start: 0.8888 (m-40) cc_final: 0.8152 (m-40) REVERT: B 1064 ARG cc_start: 0.8520 (ttp80) cc_final: 0.8290 (ttm110) REVERT: B 1067 ARG cc_start: 0.8555 (tmm-80) cc_final: 0.7867 (ttt90) REVERT: B 1080 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7225 (tt) REVERT: B 1130 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8572 (mt-10) REVERT: C 173 HIS cc_start: 0.8823 (t-170) cc_final: 0.8340 (t-170) REVERT: C 251 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.5919 (mt) REVERT: C 397 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9004 (pt) REVERT: C 509 MET cc_start: 0.6361 (ttt) cc_final: 0.5791 (mmp) REVERT: C 595 LEU cc_start: 0.9120 (mp) cc_final: 0.8866 (mp) REVERT: C 601 ARG cc_start: 0.8663 (mtp-110) cc_final: 0.7840 (mtt180) REVERT: C 615 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8899 (tp) REVERT: C 629 GLU cc_start: 0.8623 (tt0) cc_final: 0.8154 (tt0) REVERT: C 656 GLN cc_start: 0.8584 (mt0) cc_final: 0.8323 (mt0) REVERT: C 660 GLN cc_start: 0.8659 (mp10) cc_final: 0.8091 (mt0) REVERT: C 699 CYS cc_start: 0.7835 (m) cc_final: 0.7594 (t) REVERT: C 710 PHE cc_start: 0.8421 (m-80) cc_final: 0.8181 (m-80) REVERT: C 776 TRP cc_start: 0.8268 (m100) cc_final: 0.7647 (m100) REVERT: C 784 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8794 (ttp) REVERT: C 804 ASP cc_start: 0.7461 (t0) cc_final: 0.6896 (t0) REVERT: C 866 GLN cc_start: 0.8512 (mt0) cc_final: 0.8263 (mt0) REVERT: C 879 VAL cc_start: 0.8869 (t) cc_final: 0.8616 (t) REVERT: C 892 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8087 (ttm-80) REVERT: C 1067 ARG cc_start: 0.8623 (ttp80) cc_final: 0.8042 (ttt90) REVERT: C 1080 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7634 (mt) REVERT: C 1160 LYS cc_start: 0.9009 (mmtp) cc_final: 0.8762 (mmtp) REVERT: D 113 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7907 (ttp80) REVERT: D 175 MET cc_start: 0.7725 (ptm) cc_final: 0.7386 (ppp) REVERT: D 454 PHE cc_start: 0.7755 (t80) cc_final: 0.7466 (t80) REVERT: D 509 MET cc_start: 0.6359 (ttt) cc_final: 0.5660 (mmp) REVERT: D 577 TYR cc_start: 0.9183 (t80) cc_final: 0.8974 (t80) REVERT: D 594 LEU cc_start: 0.9542 (tp) cc_final: 0.9268 (tp) REVERT: D 601 ARG cc_start: 0.8656 (mtp-110) cc_final: 0.7870 (mtt180) REVERT: D 629 GLU cc_start: 0.8673 (tt0) cc_final: 0.8220 (tt0) REVERT: D 656 GLN cc_start: 0.8676 (mt0) cc_final: 0.8032 (mt0) REVERT: D 659 MET cc_start: 0.8798 (ptm) cc_final: 0.8583 (ptm) REVERT: D 660 GLN cc_start: 0.8585 (mp10) cc_final: 0.7816 (mp10) REVERT: D 710 PHE cc_start: 0.8548 (m-80) cc_final: 0.8332 (m-80) REVERT: D 892 ARG cc_start: 0.8383 (ttt180) cc_final: 0.8104 (ttt90) REVERT: D 1064 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8299 (ttm110) REVERT: D 1067 ARG cc_start: 0.8630 (ttp80) cc_final: 0.8020 (ttt90) REVERT: D 1080 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7504 (mt) REVERT: D 1129 LYS cc_start: 0.8836 (ttpt) cc_final: 0.8606 (ttpt) REVERT: D 1160 LYS cc_start: 0.9041 (mmtp) cc_final: 0.8778 (mmtp) outliers start: 138 outliers final: 50 residues processed: 974 average time/residue: 0.2159 time to fit residues: 329.4034 Evaluate side-chains 797 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 733 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 601 ARG Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 914 LYS Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 914 LYS Chi-restraints excluded: chain C residue 1080 ILE Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 598 VAL Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 914 LYS Chi-restraints excluded: chain D residue 1080 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 207 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 269 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 270 optimal weight: 0.5980 chunk 171 optimal weight: 0.8980 chunk 293 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 GLN A 570 ASN A 573 GLN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 GLN B 228 ASN B 295 GLN B 447 HIS B 462 GLN B 570 ASN B 573 GLN B 786 ASN B1070 HIS B1164 HIS C 165 HIS ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 GLN C 570 ASN C 573 GLN C 786 ASN C1017 ASN C1084 HIS ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 GLN D 228 ASN D 573 GLN D 673 GLN D 786 ASN D 866 GLN D1017 ASN D1084 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.179120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.125859 restraints weight = 47458.713| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.65 r_work: 0.3365 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30824 Z= 0.169 Angle : 0.722 11.325 41844 Z= 0.350 Chirality : 0.042 0.251 4716 Planarity : 0.006 0.066 5252 Dihedral : 7.080 58.443 5022 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.34 % Favored : 91.55 % Rotamer: Outliers : 4.95 % Allowed : 19.69 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.13), residues: 3728 helix: -0.29 (0.10), residues: 2368 sheet: -4.15 (0.27), residues: 184 loop : -3.02 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 405 TYR 0.017 0.002 TYR A1057 PHE 0.032 0.002 PHE B1069 TRP 0.025 0.002 TRP A 152 HIS 0.017 0.001 HIS B1070 Details of bonding type rmsd covalent geometry : bond 0.00390 (30820) covalent geometry : angle 0.72157 (41836) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.61252 ( 8) hydrogen bonds : bond 0.03985 ( 1510) hydrogen bonds : angle 4.50443 ( 4470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 815 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.6994 (tt) REVERT: A 186 MET cc_start: 0.8038 (mpt) cc_final: 0.7628 (mpt) REVERT: A 260 GLN cc_start: 0.8092 (mm110) cc_final: 0.7829 (mm110) REVERT: A 281 ASP cc_start: 0.7984 (m-30) cc_final: 0.7371 (p0) REVERT: A 284 MET cc_start: 0.5875 (tpp) cc_final: 0.5613 (ttp) REVERT: A 358 LYS cc_start: 0.5964 (OUTLIER) cc_final: 0.5681 (ttmt) REVERT: A 431 ASP cc_start: 0.9231 (m-30) cc_final: 0.9001 (m-30) REVERT: A 509 MET cc_start: 0.6587 (ttt) cc_final: 0.5815 (mmp) REVERT: A 590 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9023 (mm) REVERT: A 601 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.8190 (ptm160) REVERT: A 629 GLU cc_start: 0.8882 (tt0) cc_final: 0.8534 (tt0) REVERT: A 656 GLN cc_start: 0.8662 (mt0) cc_final: 0.8007 (mt0) REVERT: A 660 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8191 (mp-120) REVERT: A 776 TRP cc_start: 0.8508 (m100) cc_final: 0.8263 (m100) REVERT: A 804 ASP cc_start: 0.7640 (t0) cc_final: 0.7382 (t0) REVERT: A 813 LEU cc_start: 0.8759 (mt) cc_final: 0.8528 (mt) REVERT: A 857 ARG cc_start: 0.7131 (ttm110) cc_final: 0.6732 (ptp-110) REVERT: A 1029 LEU cc_start: 0.9512 (tp) cc_final: 0.9170 (tp) REVERT: A 1067 ARG cc_start: 0.8600 (tmm-80) cc_final: 0.8015 (ttt90) REVERT: A 1080 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7477 (tt) REVERT: A 1161 GLN cc_start: 0.8865 (mm110) cc_final: 0.8657 (mt0) REVERT: B 186 MET cc_start: 0.8213 (mpt) cc_final: 0.7747 (mpt) REVERT: B 372 GLU cc_start: 0.8432 (mp0) cc_final: 0.8047 (pm20) REVERT: B 397 LEU cc_start: 0.9322 (tt) cc_final: 0.9074 (pt) REVERT: B 509 MET cc_start: 0.6621 (ttt) cc_final: 0.5804 (mmp) REVERT: B 594 LEU cc_start: 0.9583 (tp) cc_final: 0.9308 (tp) REVERT: B 595 LEU cc_start: 0.9285 (mp) cc_final: 0.9077 (mp) REVERT: B 601 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7437 (mtt180) REVERT: B 629 GLU cc_start: 0.8762 (tt0) cc_final: 0.8361 (tt0) REVERT: B 633 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8537 (p) REVERT: B 767 ARG cc_start: 0.7350 (tmm160) cc_final: 0.7103 (tmm160) REVERT: B 819 PHE cc_start: 0.8749 (t80) cc_final: 0.8444 (t80) REVERT: B 828 GLU cc_start: 0.8098 (tp30) cc_final: 0.7264 (tm-30) REVERT: B 865 ASN cc_start: 0.8896 (m-40) cc_final: 0.8606 (m-40) REVERT: B 1067 ARG cc_start: 0.8578 (tmm-80) cc_final: 0.8006 (ttt90) REVERT: B 1129 LYS cc_start: 0.8955 (ttpt) cc_final: 0.8710 (ttpt) REVERT: C 173 HIS cc_start: 0.8773 (t-170) cc_final: 0.8370 (t-170) REVERT: C 186 MET cc_start: 0.8420 (mpt) cc_final: 0.8152 (mpt) REVERT: C 249 PHE cc_start: 0.8043 (t80) cc_final: 0.7834 (t80) REVERT: C 397 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8987 (pp) REVERT: C 431 ASP cc_start: 0.8985 (m-30) cc_final: 0.8761 (m-30) REVERT: C 509 MET cc_start: 0.6488 (ttt) cc_final: 0.5698 (mmp) REVERT: C 576 MET cc_start: 0.8908 (tpp) cc_final: 0.8634 (tpp) REVERT: C 595 LEU cc_start: 0.9227 (mp) cc_final: 0.9005 (mp) REVERT: C 601 ARG cc_start: 0.8689 (mtp-110) cc_final: 0.8323 (ptm160) REVERT: C 629 GLU cc_start: 0.8676 (tt0) cc_final: 0.8290 (tt0) REVERT: C 656 GLN cc_start: 0.8711 (mt0) cc_final: 0.8321 (mt0) REVERT: C 660 GLN cc_start: 0.8742 (mp10) cc_final: 0.8139 (mt0) REVERT: C 784 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8757 (ttp) REVERT: C 804 ASP cc_start: 0.7478 (t0) cc_final: 0.6989 (t0) REVERT: C 827 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7784 (tp30) REVERT: C 892 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8227 (ttt90) REVERT: C 1017 ASN cc_start: 0.8426 (OUTLIER) cc_final: 0.8149 (t0) REVERT: C 1038 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9259 (tp) REVERT: C 1067 ARG cc_start: 0.8543 (ttp80) cc_final: 0.8112 (ttt90) REVERT: C 1160 LYS cc_start: 0.9003 (mmtp) cc_final: 0.8762 (mmtp) REVERT: D 113 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7834 (ttp80) REVERT: D 186 MET cc_start: 0.8374 (mpt) cc_final: 0.8127 (mpt) REVERT: D 374 GLU cc_start: 0.7995 (tt0) cc_final: 0.7549 (tt0) REVERT: D 509 MET cc_start: 0.6508 (ttt) cc_final: 0.5658 (mmp) REVERT: D 577 TYR cc_start: 0.9168 (t80) cc_final: 0.8895 (t80) REVERT: D 594 LEU cc_start: 0.9500 (tp) cc_final: 0.9231 (tp) REVERT: D 595 LEU cc_start: 0.9264 (mp) cc_final: 0.9050 (mp) REVERT: D 601 ARG cc_start: 0.8659 (mtp-110) cc_final: 0.7856 (mtt180) REVERT: D 615 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8975 (tp) REVERT: D 629 GLU cc_start: 0.8706 (tt0) cc_final: 0.8194 (tt0) REVERT: D 656 GLN cc_start: 0.8765 (mt0) cc_final: 0.8341 (mt0) REVERT: D 660 GLN cc_start: 0.8674 (mp10) cc_final: 0.7968 (mt0) REVERT: D 767 ARG cc_start: 0.7366 (tmm160) cc_final: 0.7130 (tmm160) REVERT: D 776 TRP cc_start: 0.8401 (m100) cc_final: 0.7974 (m100) REVERT: D 815 LEU cc_start: 0.9100 (mt) cc_final: 0.8870 (mt) REVERT: D 819 PHE cc_start: 0.8747 (t80) cc_final: 0.8484 (t80) REVERT: D 827 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7746 (tp30) REVERT: D 828 GLU cc_start: 0.8145 (tp30) cc_final: 0.7828 (tp30) REVERT: D 882 ARG cc_start: 0.8862 (ttp80) cc_final: 0.8473 (ttp80) REVERT: D 892 ARG cc_start: 0.8405 (ttt180) cc_final: 0.8139 (ttt90) REVERT: D 1067 ARG cc_start: 0.8529 (ttp80) cc_final: 0.8055 (ttt90) REVERT: D 1129 LYS cc_start: 0.8930 (ttpt) cc_final: 0.8465 (ptmm) REVERT: D 1154 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8901 (mtmm) REVERT: D 1160 LYS cc_start: 0.8997 (mmtp) cc_final: 0.8781 (mmtp) outliers start: 153 outliers final: 65 residues processed: 897 average time/residue: 0.2148 time to fit residues: 302.9734 Evaluate side-chains 806 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 727 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 590 LEU Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 570 ASN Chi-restraints excluded: chain B residue 601 ARG Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 798 SER Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 570 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 784 MET Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 863 SER Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1121 LEU Chi-restraints excluded: chain D residue 1154 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 210 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 312 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 219 optimal weight: 8.9990 chunk 180 optimal weight: 3.9990 chunk 104 optimal weight: 0.0470 chunk 329 optimal weight: 0.8980 chunk 332 optimal weight: 0.3980 chunk 319 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 573 GLN A 786 ASN A1037 ASN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN B 573 GLN B 786 ASN B 980 GLN B1037 ASN B1070 HIS B1084 HIS B1128 HIS C 570 ASN C 573 GLN C 786 ASN ** C1017 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 GLN D 573 GLN D 786 ASN D 866 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.180301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127932 restraints weight = 47291.483| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.62 r_work: 0.3399 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30824 Z= 0.135 Angle : 0.686 11.246 41844 Z= 0.328 Chirality : 0.040 0.169 4716 Planarity : 0.005 0.064 5252 Dihedral : 6.718 59.389 5006 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.15 % Favored : 91.74 % Rotamer: Outliers : 4.08 % Allowed : 20.79 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3728 helix: 0.27 (0.10), residues: 2388 sheet: -3.60 (0.36), residues: 144 loop : -2.84 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1064 TYR 0.015 0.002 TYR B1057 PHE 0.030 0.002 PHE A 454 TRP 0.020 0.002 TRP D 133 HIS 0.012 0.001 HIS B1070 Details of bonding type rmsd covalent geometry : bond 0.00311 (30820) covalent geometry : angle 0.68578 (41836) SS BOND : bond 0.00047 ( 4) SS BOND : angle 0.45859 ( 8) hydrogen bonds : bond 0.03658 ( 1510) hydrogen bonds : angle 4.27065 ( 4470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 819 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 HIS cc_start: 0.8740 (t-170) cc_final: 0.8524 (t70) REVERT: A 186 MET cc_start: 0.8016 (mpt) cc_final: 0.7562 (mpt) REVERT: A 260 GLN cc_start: 0.7965 (mm110) cc_final: 0.7725 (mm110) REVERT: A 281 ASP cc_start: 0.8060 (m-30) cc_final: 0.7505 (p0) REVERT: A 284 MET cc_start: 0.5983 (tpp) cc_final: 0.5552 (ttp) REVERT: A 431 ASP cc_start: 0.9154 (m-30) cc_final: 0.8906 (m-30) REVERT: A 509 MET cc_start: 0.6587 (ttt) cc_final: 0.5821 (mmp) REVERT: A 629 GLU cc_start: 0.8887 (tt0) cc_final: 0.8492 (tt0) REVERT: A 776 TRP cc_start: 0.8499 (m100) cc_final: 0.8248 (m100) REVERT: A 804 ASP cc_start: 0.7501 (t0) cc_final: 0.7270 (t0) REVERT: A 813 LEU cc_start: 0.8770 (mt) cc_final: 0.8548 (mt) REVERT: A 857 ARG cc_start: 0.6916 (ttm110) cc_final: 0.6479 (ptp-110) REVERT: A 892 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.8319 (ttt90) REVERT: A 1029 LEU cc_start: 0.9492 (tp) cc_final: 0.9073 (tp) REVERT: A 1038 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9160 (tp) REVERT: A 1067 ARG cc_start: 0.8497 (tmm-80) cc_final: 0.8006 (ttt90) REVERT: A 1080 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7391 (tt) REVERT: A 1129 LYS cc_start: 0.8965 (ttpt) cc_final: 0.8177 (ptmt) REVERT: A 1138 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8312 (ttm110) REVERT: B 186 MET cc_start: 0.8380 (mpt) cc_final: 0.7907 (mpt) REVERT: B 372 GLU cc_start: 0.8461 (mp0) cc_final: 0.8013 (pm20) REVERT: B 397 LEU cc_start: 0.9299 (tt) cc_final: 0.9046 (pp) REVERT: B 436 ASP cc_start: 0.8400 (t70) cc_final: 0.8077 (t70) REVERT: B 472 LEU cc_start: 0.8162 (tt) cc_final: 0.7849 (mt) REVERT: B 509 MET cc_start: 0.6752 (ttt) cc_final: 0.5910 (mmp) REVERT: B 594 LEU cc_start: 0.9510 (tp) cc_final: 0.9252 (tp) REVERT: B 629 GLU cc_start: 0.8803 (tt0) cc_final: 0.8303 (tt0) REVERT: B 819 PHE cc_start: 0.8746 (t80) cc_final: 0.8305 (t80) REVERT: B 1067 ARG cc_start: 0.8516 (tmm-80) cc_final: 0.8029 (ttt90) REVERT: B 1080 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6764 (mt) REVERT: B 1129 LYS cc_start: 0.8967 (ttpt) cc_final: 0.8260 (ptmt) REVERT: C 186 MET cc_start: 0.8390 (mpt) cc_final: 0.7997 (mpt) REVERT: C 249 PHE cc_start: 0.8003 (t80) cc_final: 0.7780 (t80) REVERT: C 397 LEU cc_start: 0.9250 (tt) cc_final: 0.9009 (pp) REVERT: C 431 ASP cc_start: 0.8969 (m-30) cc_final: 0.8736 (m-30) REVERT: C 436 ASP cc_start: 0.8316 (t70) cc_final: 0.8046 (t70) REVERT: C 509 MET cc_start: 0.6571 (ttt) cc_final: 0.5701 (mmp) REVERT: C 595 LEU cc_start: 0.9262 (mp) cc_final: 0.9035 (mp) REVERT: C 615 LEU cc_start: 0.9332 (tp) cc_final: 0.9114 (tp) REVERT: C 629 GLU cc_start: 0.8666 (tt0) cc_final: 0.8158 (tt0) REVERT: C 656 GLN cc_start: 0.8711 (mt0) cc_final: 0.8300 (mt0) REVERT: C 660 GLN cc_start: 0.8796 (mp10) cc_final: 0.8177 (mp10) REVERT: C 776 TRP cc_start: 0.8448 (m100) cc_final: 0.8241 (m100) REVERT: C 804 ASP cc_start: 0.7442 (t0) cc_final: 0.6970 (t0) REVERT: C 819 PHE cc_start: 0.8787 (t80) cc_final: 0.8582 (t80) REVERT: C 827 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7674 (tp30) REVERT: C 873 THR cc_start: 0.8699 (t) cc_final: 0.8480 (t) REVERT: C 892 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.8202 (ttm-80) REVERT: C 1038 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9253 (tp) REVERT: C 1067 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8050 (ttt90) REVERT: C 1116 GLU cc_start: 0.7850 (pp20) cc_final: 0.7648 (tm-30) REVERT: C 1160 LYS cc_start: 0.8957 (mmtp) cc_final: 0.8733 (mmtp) REVERT: D 113 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7883 (ttp80) REVERT: D 186 MET cc_start: 0.8300 (mpt) cc_final: 0.7941 (mpt) REVERT: D 259 GLN cc_start: 0.6483 (mm110) cc_final: 0.6177 (mt0) REVERT: D 374 GLU cc_start: 0.7658 (tt0) cc_final: 0.7447 (tt0) REVERT: D 420 TRP cc_start: 0.4740 (m100) cc_final: 0.4480 (m100) REVERT: D 509 MET cc_start: 0.6610 (ttt) cc_final: 0.5664 (mmp) REVERT: D 577 TYR cc_start: 0.9122 (t80) cc_final: 0.8863 (t80) REVERT: D 594 LEU cc_start: 0.9476 (tp) cc_final: 0.9218 (tp) REVERT: D 595 LEU cc_start: 0.9263 (mp) cc_final: 0.9062 (mp) REVERT: D 601 ARG cc_start: 0.8663 (mtp-110) cc_final: 0.8408 (ptm160) REVERT: D 615 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8944 (tp) REVERT: D 629 GLU cc_start: 0.8731 (tt0) cc_final: 0.8317 (tt0) REVERT: D 656 GLN cc_start: 0.8703 (mt0) cc_final: 0.8259 (mt0) REVERT: D 660 GLN cc_start: 0.8680 (mp10) cc_final: 0.7997 (mt0) REVERT: D 776 TRP cc_start: 0.8453 (m100) cc_final: 0.7997 (m100) REVERT: D 804 ASP cc_start: 0.7414 (t0) cc_final: 0.7025 (t0) REVERT: D 819 PHE cc_start: 0.8822 (t80) cc_final: 0.8535 (t80) REVERT: D 827 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7618 (tp30) REVERT: D 882 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8543 (ttp80) REVERT: D 892 ARG cc_start: 0.8385 (ttt180) cc_final: 0.8164 (ttt90) REVERT: D 1064 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8221 (ttp-110) REVERT: D 1067 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8046 (ttt90) REVERT: D 1129 LYS cc_start: 0.8934 (ttpt) cc_final: 0.8187 (ptmm) REVERT: D 1154 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8845 (mtmm) REVERT: D 1160 LYS cc_start: 0.8953 (mmtp) cc_final: 0.8723 (mmtp) outliers start: 126 outliers final: 74 residues processed: 891 average time/residue: 0.1991 time to fit residues: 280.3695 Evaluate side-chains 827 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 745 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1081 VAL Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1134 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 863 SER Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1154 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 303 optimal weight: 0.7980 chunk 350 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 224 optimal weight: 0.2980 chunk 118 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 ASN A 573 GLN A 656 GLN A 786 ASN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN B 573 GLN B 786 ASN C 260 GLN C 570 ASN C 573 GLN C1017 ASN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1128 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.176885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.124142 restraints weight = 47332.434| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.59 r_work: 0.3338 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30824 Z= 0.172 Angle : 0.687 9.564 41844 Z= 0.333 Chirality : 0.041 0.188 4716 Planarity : 0.005 0.073 5252 Dihedral : 6.522 59.795 5006 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.34 % Favored : 91.55 % Rotamer: Outliers : 4.53 % Allowed : 21.70 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 3728 helix: 0.60 (0.11), residues: 2364 sheet: -3.67 (0.33), residues: 184 loop : -2.77 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 171 TYR 0.017 0.002 TYR D 944 PHE 0.023 0.002 PHE A 454 TRP 0.025 0.002 TRP A 133 HIS 0.022 0.001 HIS B1070 Details of bonding type rmsd covalent geometry : bond 0.00403 (30820) covalent geometry : angle 0.68652 (41836) SS BOND : bond 0.00021 ( 4) SS BOND : angle 0.61718 ( 8) hydrogen bonds : bond 0.03832 ( 1510) hydrogen bonds : angle 4.23564 ( 4470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 799 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 HIS cc_start: 0.8762 (t-170) cc_final: 0.8431 (t70) REVERT: A 186 MET cc_start: 0.8005 (mpt) cc_final: 0.7600 (mpt) REVERT: A 260 GLN cc_start: 0.7996 (mm110) cc_final: 0.7747 (mm110) REVERT: A 281 ASP cc_start: 0.8055 (m-30) cc_final: 0.7620 (p0) REVERT: A 284 MET cc_start: 0.5823 (tpp) cc_final: 0.5510 (ttp) REVERT: A 431 ASP cc_start: 0.9135 (m-30) cc_final: 0.8889 (m-30) REVERT: A 509 MET cc_start: 0.6701 (ttt) cc_final: 0.5926 (mmp) REVERT: A 611 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8568 (ttp80) REVERT: A 629 GLU cc_start: 0.8890 (tt0) cc_final: 0.8402 (tt0) REVERT: A 660 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8272 (mp-120) REVERT: A 786 ASN cc_start: 0.8646 (m110) cc_final: 0.8441 (m-40) REVERT: A 804 ASP cc_start: 0.7555 (t0) cc_final: 0.7277 (t0) REVERT: A 813 LEU cc_start: 0.8756 (mt) cc_final: 0.8543 (mt) REVERT: A 827 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7811 (tp30) REVERT: A 857 ARG cc_start: 0.6934 (ttm110) cc_final: 0.6475 (ptp-110) REVERT: A 952 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9048 (pt) REVERT: A 1029 LEU cc_start: 0.9558 (tp) cc_final: 0.9217 (tp) REVERT: A 1067 ARG cc_start: 0.8439 (tmm-80) cc_final: 0.8026 (ttt90) REVERT: A 1080 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7698 (tt) REVERT: A 1138 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8288 (ttm110) REVERT: B 171 ARG cc_start: 0.7334 (ttm170) cc_final: 0.7081 (ttp80) REVERT: B 175 MET cc_start: 0.7693 (mtm) cc_final: 0.7233 (mtm) REVERT: B 186 MET cc_start: 0.8369 (mpt) cc_final: 0.7811 (mpt) REVERT: B 249 PHE cc_start: 0.8025 (t80) cc_final: 0.7798 (t80) REVERT: B 372 GLU cc_start: 0.8498 (mp0) cc_final: 0.8055 (pm20) REVERT: B 397 LEU cc_start: 0.9284 (tt) cc_final: 0.8989 (pp) REVERT: B 430 MET cc_start: 0.7904 (mmm) cc_final: 0.7386 (tpp) REVERT: B 509 MET cc_start: 0.6826 (ttt) cc_final: 0.5879 (mmp) REVERT: B 594 LEU cc_start: 0.9588 (tp) cc_final: 0.9295 (tp) REVERT: B 629 GLU cc_start: 0.8776 (tt0) cc_final: 0.8339 (tt0) REVERT: B 633 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8607 (p) REVERT: B 952 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8955 (pt) REVERT: B 1067 ARG cc_start: 0.8498 (tmm-80) cc_final: 0.8062 (ttt90) REVERT: B 1080 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7131 (mt) REVERT: C 173 HIS cc_start: 0.8789 (t-170) cc_final: 0.8365 (t-170) REVERT: C 186 MET cc_start: 0.8286 (mpt) cc_final: 0.7951 (mpt) REVERT: C 249 PHE cc_start: 0.8100 (t80) cc_final: 0.7881 (t80) REVERT: C 397 LEU cc_start: 0.9296 (tt) cc_final: 0.8995 (pp) REVERT: C 431 ASP cc_start: 0.9060 (m-30) cc_final: 0.8806 (m-30) REVERT: C 509 MET cc_start: 0.6668 (ttt) cc_final: 0.5750 (mmp) REVERT: C 580 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8786 (mt-10) REVERT: C 629 GLU cc_start: 0.8709 (tt0) cc_final: 0.8167 (tt0) REVERT: C 776 TRP cc_start: 0.8527 (m100) cc_final: 0.8231 (m100) REVERT: C 804 ASP cc_start: 0.7535 (t0) cc_final: 0.7294 (t0) REVERT: C 813 LEU cc_start: 0.8697 (mt) cc_final: 0.8444 (mt) REVERT: C 857 ARG cc_start: 0.6918 (ttm110) cc_final: 0.6485 (ptp-110) REVERT: C 1023 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9278 (mp) REVERT: C 1067 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8084 (ttt90) REVERT: C 1160 LYS cc_start: 0.8986 (mmtp) cc_final: 0.8746 (mmtp) REVERT: D 113 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7833 (ttp80) REVERT: D 186 MET cc_start: 0.8311 (mpt) cc_final: 0.7940 (mpt) REVERT: D 259 GLN cc_start: 0.6587 (mm110) cc_final: 0.6189 (mt0) REVERT: D 436 ASP cc_start: 0.8328 (t70) cc_final: 0.8103 (t70) REVERT: D 509 MET cc_start: 0.6673 (ttt) cc_final: 0.5709 (mmp) REVERT: D 577 TYR cc_start: 0.9147 (t80) cc_final: 0.8880 (t80) REVERT: D 594 LEU cc_start: 0.9574 (tp) cc_final: 0.9300 (tp) REVERT: D 601 ARG cc_start: 0.8683 (mtp-110) cc_final: 0.8453 (ptm160) REVERT: D 629 GLU cc_start: 0.8769 (tt0) cc_final: 0.8300 (tt0) REVERT: D 656 GLN cc_start: 0.8821 (mt0) cc_final: 0.8612 (mt0) REVERT: D 804 ASP cc_start: 0.7415 (t0) cc_final: 0.7035 (t0) REVERT: D 819 PHE cc_start: 0.8874 (t80) cc_final: 0.8361 (t80) REVERT: D 827 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7500 (tp30) REVERT: D 882 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8545 (ttp80) REVERT: D 1067 ARG cc_start: 0.8423 (ttp80) cc_final: 0.8098 (ttt90) REVERT: D 1116 GLU cc_start: 0.7950 (pp20) cc_final: 0.7677 (tm-30) REVERT: D 1118 GLU cc_start: 0.8418 (tp30) cc_final: 0.8191 (tp30) REVERT: D 1129 LYS cc_start: 0.9018 (ttpt) cc_final: 0.8354 (ptmm) REVERT: D 1154 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8735 (mtmm) REVERT: D 1160 LYS cc_start: 0.8974 (mmtp) cc_final: 0.8737 (mmtp) outliers start: 140 outliers final: 96 residues processed: 877 average time/residue: 0.1923 time to fit residues: 268.5324 Evaluate side-chains 849 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 743 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 570 ASN Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1121 LEU Chi-restraints excluded: chain C residue 1134 LEU Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1125 GLU Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1154 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 308 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 268 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 167 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 573 GLN A 656 GLN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1164 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS B 570 ASN B 573 GLN B1070 HIS ** B1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 ASN C 573 GLN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.178129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125877 restraints weight = 47229.560| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.51 r_work: 0.3364 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30824 Z= 0.146 Angle : 0.670 8.158 41844 Z= 0.324 Chirality : 0.041 0.181 4716 Planarity : 0.005 0.060 5252 Dihedral : 6.371 59.927 5004 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 92.01 % Rotamer: Outliers : 4.83 % Allowed : 22.64 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3728 helix: 0.77 (0.11), residues: 2372 sheet: -3.59 (0.34), residues: 184 loop : -2.67 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1064 TYR 0.014 0.001 TYR D1063 PHE 0.021 0.001 PHE B 578 TRP 0.019 0.002 TRP B 680 HIS 0.009 0.001 HIS A 447 Details of bonding type rmsd covalent geometry : bond 0.00341 (30820) covalent geometry : angle 0.66970 (41836) SS BOND : bond 0.00027 ( 4) SS BOND : angle 0.51633 ( 8) hydrogen bonds : bond 0.03682 ( 1510) hydrogen bonds : angle 4.14923 ( 4470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 800 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 HIS cc_start: 0.8783 (t-170) cc_final: 0.8460 (t70) REVERT: A 186 MET cc_start: 0.7944 (mpt) cc_final: 0.7612 (mpt) REVERT: A 260 GLN cc_start: 0.7906 (mm110) cc_final: 0.7626 (mm110) REVERT: A 281 ASP cc_start: 0.8042 (m-30) cc_final: 0.7659 (p0) REVERT: A 284 MET cc_start: 0.5961 (tpp) cc_final: 0.5574 (ttp) REVERT: A 431 ASP cc_start: 0.9116 (m-30) cc_final: 0.8869 (m-30) REVERT: A 509 MET cc_start: 0.6813 (ttt) cc_final: 0.6032 (mmp) REVERT: A 629 GLU cc_start: 0.8851 (tt0) cc_final: 0.8445 (tt0) REVERT: A 656 GLN cc_start: 0.8779 (mt0) cc_final: 0.7680 (mp10) REVERT: A 660 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8243 (mp-120) REVERT: A 804 ASP cc_start: 0.7445 (t0) cc_final: 0.7092 (t0) REVERT: A 813 LEU cc_start: 0.8757 (mt) cc_final: 0.8543 (mt) REVERT: A 827 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7731 (tp30) REVERT: A 857 ARG cc_start: 0.6922 (ttm110) cc_final: 0.6456 (ptp-110) REVERT: A 952 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9023 (pt) REVERT: A 1029 LEU cc_start: 0.9556 (tp) cc_final: 0.9211 (tp) REVERT: A 1067 ARG cc_start: 0.8338 (tmm-80) cc_final: 0.7973 (ttt90) REVERT: A 1080 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7643 (tt) REVERT: A 1138 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8319 (ttm110) REVERT: B 186 MET cc_start: 0.8314 (mpt) cc_final: 0.7904 (mpt) REVERT: B 249 PHE cc_start: 0.8079 (t80) cc_final: 0.7872 (t80) REVERT: B 372 GLU cc_start: 0.8578 (mp0) cc_final: 0.8286 (pm20) REVERT: B 430 MET cc_start: 0.8072 (mmm) cc_final: 0.7487 (tpt) REVERT: B 509 MET cc_start: 0.6649 (ttt) cc_final: 0.5713 (mmp) REVERT: B 594 LEU cc_start: 0.9576 (tp) cc_final: 0.9304 (tp) REVERT: B 629 GLU cc_start: 0.8792 (tt0) cc_final: 0.8274 (tt0) REVERT: B 804 ASP cc_start: 0.7355 (t0) cc_final: 0.6901 (t0) REVERT: B 952 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8965 (pt) REVERT: B 1059 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8111 (mmtp) REVERT: B 1067 ARG cc_start: 0.8412 (tmm-80) cc_final: 0.7999 (ttt90) REVERT: B 1080 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.7025 (mt) REVERT: C 113 ARG cc_start: 0.8478 (ttt-90) cc_final: 0.8190 (ttt-90) REVERT: C 173 HIS cc_start: 0.8799 (t-170) cc_final: 0.8387 (t-170) REVERT: C 186 MET cc_start: 0.8118 (mpt) cc_final: 0.7915 (mpt) REVERT: C 249 PHE cc_start: 0.8114 (t80) cc_final: 0.7819 (t80) REVERT: C 315 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7378 (tm) REVERT: C 430 MET cc_start: 0.8224 (mmm) cc_final: 0.7652 (tpt) REVERT: C 431 ASP cc_start: 0.9001 (m-30) cc_final: 0.8758 (m-30) REVERT: C 509 MET cc_start: 0.6760 (ttt) cc_final: 0.5847 (mmp) REVERT: C 607 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: C 611 ARG cc_start: 0.8613 (ttm110) cc_final: 0.8361 (ttp80) REVERT: C 629 GLU cc_start: 0.8686 (tt0) cc_final: 0.8190 (tt0) REVERT: C 776 TRP cc_start: 0.8353 (m100) cc_final: 0.8106 (m100) REVERT: C 804 ASP cc_start: 0.7471 (t0) cc_final: 0.7240 (t0) REVERT: C 813 LEU cc_start: 0.8721 (mt) cc_final: 0.8487 (mt) REVERT: C 827 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7557 (tp30) REVERT: C 857 ARG cc_start: 0.6892 (ttm110) cc_final: 0.6409 (ptp-110) REVERT: C 892 ARG cc_start: 0.8601 (ttt180) cc_final: 0.8269 (ttt90) REVERT: C 1059 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8139 (mmtp) REVERT: C 1067 ARG cc_start: 0.8361 (ttp80) cc_final: 0.8068 (ttt90) REVERT: C 1116 GLU cc_start: 0.7801 (pp20) cc_final: 0.7573 (tm-30) REVERT: C 1160 LYS cc_start: 0.8982 (mmtp) cc_final: 0.8738 (mmtp) REVERT: D 113 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7960 (ttp80) REVERT: D 186 MET cc_start: 0.8122 (mpt) cc_final: 0.7866 (mpt) REVERT: D 315 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7129 (tm) REVERT: D 316 GLU cc_start: 0.7886 (mp0) cc_final: 0.7621 (mp0) REVERT: D 509 MET cc_start: 0.6691 (ttt) cc_final: 0.5764 (mmp) REVERT: D 577 TYR cc_start: 0.9087 (t80) cc_final: 0.8820 (t80) REVERT: D 594 LEU cc_start: 0.9554 (tp) cc_final: 0.9285 (tp) REVERT: D 601 ARG cc_start: 0.8569 (mtp-110) cc_final: 0.8304 (ptm160) REVERT: D 629 GLU cc_start: 0.8770 (tt0) cc_final: 0.8314 (tt0) REVERT: D 804 ASP cc_start: 0.7368 (t0) cc_final: 0.6958 (t0) REVERT: D 819 PHE cc_start: 0.8935 (t80) cc_final: 0.8444 (t80) REVERT: D 882 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8496 (ttp80) REVERT: D 1067 ARG cc_start: 0.8339 (ttp80) cc_final: 0.8055 (ttt90) REVERT: D 1129 LYS cc_start: 0.8947 (ttpt) cc_final: 0.8291 (ptmm) outliers start: 149 outliers final: 102 residues processed: 885 average time/residue: 0.1963 time to fit residues: 277.0522 Evaluate side-chains 870 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 756 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 570 ASN Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1059 LYS Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain B residue 1134 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 570 ASN Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1059 LYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1134 LEU Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1154 LYS Chi-restraints excluded: chain D residue 1162 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 353 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 185 optimal weight: 0.6980 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 323 optimal weight: 6.9990 chunk 325 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN B 786 ASN B 831 GLN ** B1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1128 HIS C 404 ASN C 570 ASN C 573 GLN ** C 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1128 HIS ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN D1128 HIS D1164 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.177862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129836 restraints weight = 47135.666| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.51 r_work: 0.3369 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30824 Z= 0.149 Angle : 0.685 13.094 41844 Z= 0.331 Chirality : 0.041 0.231 4716 Planarity : 0.005 0.053 5252 Dihedral : 6.293 56.323 5004 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.23 % Favored : 91.66 % Rotamer: Outliers : 4.66 % Allowed : 23.45 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3728 helix: 0.88 (0.11), residues: 2364 sheet: -3.56 (0.32), residues: 192 loop : -2.57 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 171 TYR 0.015 0.001 TYR D1057 PHE 0.031 0.002 PHE C 414 TRP 0.024 0.002 TRP D 133 HIS 0.014 0.001 HIS B1070 Details of bonding type rmsd covalent geometry : bond 0.00349 (30820) covalent geometry : angle 0.68517 (41836) SS BOND : bond 0.00033 ( 4) SS BOND : angle 0.55552 ( 8) hydrogen bonds : bond 0.03711 ( 1510) hydrogen bonds : angle 4.17033 ( 4470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 781 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 HIS cc_start: 0.8702 (t-170) cc_final: 0.8382 (t-170) REVERT: A 186 MET cc_start: 0.7911 (mpt) cc_final: 0.7532 (mpt) REVERT: A 254 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7736 (mt-10) REVERT: A 260 GLN cc_start: 0.7905 (mm110) cc_final: 0.7654 (mm110) REVERT: A 281 ASP cc_start: 0.8038 (m-30) cc_final: 0.7669 (p0) REVERT: A 284 MET cc_start: 0.5929 (tpp) cc_final: 0.5509 (ttp) REVERT: A 431 ASP cc_start: 0.9083 (m-30) cc_final: 0.8827 (m-30) REVERT: A 629 GLU cc_start: 0.8828 (tt0) cc_final: 0.8445 (tt0) REVERT: A 660 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8322 (mp-120) REVERT: A 804 ASP cc_start: 0.7461 (t0) cc_final: 0.7067 (t0) REVERT: A 813 LEU cc_start: 0.8757 (mt) cc_final: 0.8550 (mt) REVERT: A 827 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7934 (tp30) REVERT: A 857 ARG cc_start: 0.6923 (ttm110) cc_final: 0.6463 (ptp-110) REVERT: A 952 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9035 (pt) REVERT: A 1029 LEU cc_start: 0.9556 (tp) cc_final: 0.9215 (tp) REVERT: A 1067 ARG cc_start: 0.8283 (tmm-80) cc_final: 0.7975 (ttt90) REVERT: A 1138 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8303 (ttm110) REVERT: B 186 MET cc_start: 0.8282 (mpt) cc_final: 0.7928 (mpt) REVERT: B 249 PHE cc_start: 0.8170 (t80) cc_final: 0.7917 (t80) REVERT: B 372 GLU cc_start: 0.8620 (mp0) cc_final: 0.8353 (pm20) REVERT: B 397 LEU cc_start: 0.9262 (tt) cc_final: 0.9003 (tp) REVERT: B 430 MET cc_start: 0.8014 (mmm) cc_final: 0.7430 (tpt) REVERT: B 509 MET cc_start: 0.6634 (ttt) cc_final: 0.5712 (mmp) REVERT: B 580 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8718 (mt-10) REVERT: B 629 GLU cc_start: 0.8784 (tt0) cc_final: 0.8241 (tt0) REVERT: B 804 ASP cc_start: 0.7362 (t0) cc_final: 0.6900 (t0) REVERT: B 914 LYS cc_start: 0.9138 (ttpm) cc_final: 0.8924 (ttpm) REVERT: B 952 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8989 (pt) REVERT: B 1059 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8103 (mmtp) REVERT: B 1067 ARG cc_start: 0.8351 (tmm-80) cc_final: 0.7965 (ttt90) REVERT: C 113 ARG cc_start: 0.8381 (ttt-90) cc_final: 0.8126 (ttt-90) REVERT: C 173 HIS cc_start: 0.8803 (t-170) cc_final: 0.8536 (t-170) REVERT: C 232 PHE cc_start: 0.6720 (m-80) cc_final: 0.6515 (m-10) REVERT: C 249 PHE cc_start: 0.8172 (t80) cc_final: 0.7854 (t80) REVERT: C 397 LEU cc_start: 0.9240 (tt) cc_final: 0.9040 (pp) REVERT: C 430 MET cc_start: 0.8247 (mmm) cc_final: 0.7380 (tpt) REVERT: C 431 ASP cc_start: 0.9048 (m-30) cc_final: 0.8803 (m-30) REVERT: C 509 MET cc_start: 0.6754 (ttt) cc_final: 0.5843 (mmp) REVERT: C 607 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: C 611 ARG cc_start: 0.8646 (ttm110) cc_final: 0.8420 (ttp80) REVERT: C 629 GLU cc_start: 0.8714 (tt0) cc_final: 0.8264 (tt0) REVERT: C 776 TRP cc_start: 0.8339 (m100) cc_final: 0.8100 (m100) REVERT: C 813 LEU cc_start: 0.8706 (mt) cc_final: 0.8442 (mt) REVERT: C 857 ARG cc_start: 0.6843 (ttm110) cc_final: 0.6365 (ptp-110) REVERT: C 882 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8447 (tmt-80) REVERT: C 892 ARG cc_start: 0.8531 (ttt180) cc_final: 0.8177 (ttt90) REVERT: C 1067 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7997 (ttt90) REVERT: D 113 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8030 (ttp80) REVERT: D 171 ARG cc_start: 0.7453 (ttm170) cc_final: 0.7172 (ttp80) REVERT: D 186 MET cc_start: 0.8027 (mpt) cc_final: 0.7817 (mpt) REVERT: D 315 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7138 (tm) REVERT: D 316 GLU cc_start: 0.7988 (mp0) cc_final: 0.7712 (mp0) REVERT: D 430 MET cc_start: 0.8233 (mmm) cc_final: 0.7433 (tpt) REVERT: D 434 LEU cc_start: 0.9136 (mt) cc_final: 0.8914 (mt) REVERT: D 509 MET cc_start: 0.6613 (ttt) cc_final: 0.5733 (mmp) REVERT: D 577 TYR cc_start: 0.9062 (t80) cc_final: 0.8823 (t80) REVERT: D 594 LEU cc_start: 0.9570 (tp) cc_final: 0.9304 (tp) REVERT: D 601 ARG cc_start: 0.8527 (mtp-110) cc_final: 0.8193 (ptm160) REVERT: D 629 GLU cc_start: 0.8765 (tt0) cc_final: 0.8290 (tt0) REVERT: D 804 ASP cc_start: 0.7348 (t0) cc_final: 0.6911 (t0) REVERT: D 882 ARG cc_start: 0.8690 (ttp80) cc_final: 0.8453 (ttp80) REVERT: D 1029 LEU cc_start: 0.9506 (tp) cc_final: 0.9110 (tp) REVERT: D 1067 ARG cc_start: 0.8262 (ttp80) cc_final: 0.8039 (ttt90) REVERT: D 1116 GLU cc_start: 0.7744 (pp20) cc_final: 0.7475 (tm-30) REVERT: D 1129 LYS cc_start: 0.8939 (ttpt) cc_final: 0.8235 (ptmt) outliers start: 144 outliers final: 103 residues processed: 860 average time/residue: 0.2008 time to fit residues: 276.7748 Evaluate side-chains 852 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 741 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1138 ARG Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 781 THR Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1059 LYS Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 447 HIS Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 781 THR Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1154 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 278 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 307 optimal weight: 20.0000 chunk 293 optimal weight: 10.0000 chunk 296 optimal weight: 0.9980 chunk 353 optimal weight: 0.7980 chunk 99 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 573 GLN A 584 ASN A1108 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN B 831 GLN B1070 HIS ** B1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 ASN C 424 HIS C 570 ASN C 573 GLN C 656 GLN C1164 HIS ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.178751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.130210 restraints weight = 47446.884| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.68 r_work: 0.3371 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30824 Z= 0.138 Angle : 0.691 13.996 41844 Z= 0.332 Chirality : 0.041 0.283 4716 Planarity : 0.005 0.070 5252 Dihedral : 6.240 59.682 5003 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 92.01 % Rotamer: Outliers : 4.34 % Allowed : 24.00 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.14), residues: 3728 helix: 0.99 (0.11), residues: 2348 sheet: -3.49 (0.33), residues: 192 loop : -2.59 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 405 TYR 0.018 0.001 TYR D1057 PHE 0.037 0.001 PHE B 578 TRP 0.022 0.002 TRP D 133 HIS 0.010 0.001 HIS D 447 Details of bonding type rmsd covalent geometry : bond 0.00320 (30820) covalent geometry : angle 0.69144 (41836) SS BOND : bond 0.00026 ( 4) SS BOND : angle 0.48068 ( 8) hydrogen bonds : bond 0.03640 ( 1510) hydrogen bonds : angle 4.16629 ( 4470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 811 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7843 (mpt) cc_final: 0.7509 (mpt) REVERT: A 195 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.5644 (pmt-80) REVERT: A 254 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7677 (mt-10) REVERT: A 260 GLN cc_start: 0.7888 (mm110) cc_final: 0.7623 (mm110) REVERT: A 364 TYR cc_start: 0.7091 (t80) cc_final: 0.6619 (t80) REVERT: A 430 MET cc_start: 0.8074 (mmm) cc_final: 0.7764 (tpp) REVERT: A 431 ASP cc_start: 0.9067 (m-30) cc_final: 0.8866 (m-30) REVERT: A 611 ARG cc_start: 0.8854 (ttm110) cc_final: 0.8641 (ttp80) REVERT: A 629 GLU cc_start: 0.8889 (tt0) cc_final: 0.8505 (tt0) REVERT: A 660 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8732 (mp10) REVERT: A 804 ASP cc_start: 0.7471 (t0) cc_final: 0.7029 (t0) REVERT: A 813 LEU cc_start: 0.8722 (mt) cc_final: 0.8516 (mt) REVERT: A 827 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7827 (tp30) REVERT: A 857 ARG cc_start: 0.6930 (ttm110) cc_final: 0.6467 (ptp-110) REVERT: A 892 ARG cc_start: 0.8571 (ttt90) cc_final: 0.8317 (ttt90) REVERT: A 952 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9014 (pt) REVERT: A 1029 LEU cc_start: 0.9548 (tp) cc_final: 0.9178 (tp) REVERT: A 1067 ARG cc_start: 0.8257 (tmm-80) cc_final: 0.7919 (ttt90) REVERT: B 186 MET cc_start: 0.8222 (mpt) cc_final: 0.7910 (mpt) REVERT: B 249 PHE cc_start: 0.8161 (t80) cc_final: 0.7897 (t80) REVERT: B 372 GLU cc_start: 0.8649 (mp0) cc_final: 0.8367 (pm20) REVERT: B 397 LEU cc_start: 0.9243 (tt) cc_final: 0.8995 (tp) REVERT: B 430 MET cc_start: 0.8051 (mmm) cc_final: 0.7498 (tpt) REVERT: B 509 MET cc_start: 0.6657 (ttt) cc_final: 0.5643 (mmp) REVERT: B 608 GLU cc_start: 0.8624 (tp30) cc_final: 0.8262 (tp30) REVERT: B 613 LYS cc_start: 0.9064 (mtmt) cc_final: 0.8639 (mtmm) REVERT: B 629 GLU cc_start: 0.8801 (tt0) cc_final: 0.8291 (tt0) REVERT: B 804 ASP cc_start: 0.7268 (t0) cc_final: 0.6796 (t0) REVERT: B 857 ARG cc_start: 0.7062 (ttm110) cc_final: 0.6686 (ptp-110) REVERT: B 952 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8997 (pt) REVERT: B 1059 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8038 (mmtp) REVERT: B 1067 ARG cc_start: 0.8292 (tmm-80) cc_final: 0.7958 (ttt90) REVERT: C 113 ARG cc_start: 0.8510 (ttt-90) cc_final: 0.7696 (ttt-90) REVERT: C 249 PHE cc_start: 0.8176 (t80) cc_final: 0.7894 (t80) REVERT: C 315 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7294 (tm) REVERT: C 355 MET cc_start: 0.5133 (mmm) cc_final: 0.4915 (mmt) REVERT: C 397 LEU cc_start: 0.9234 (tt) cc_final: 0.9016 (pp) REVERT: C 509 MET cc_start: 0.6761 (ttt) cc_final: 0.5786 (mmp) REVERT: C 607 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: C 611 ARG cc_start: 0.8707 (ttm110) cc_final: 0.8458 (ttp80) REVERT: C 629 GLU cc_start: 0.8715 (tt0) cc_final: 0.8238 (tt0) REVERT: C 776 TRP cc_start: 0.8341 (m100) cc_final: 0.8087 (m100) REVERT: C 813 LEU cc_start: 0.8660 (mt) cc_final: 0.8444 (mt) REVERT: C 827 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7589 (tp30) REVERT: C 857 ARG cc_start: 0.6830 (ttm110) cc_final: 0.6338 (ptp-110) REVERT: C 882 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8595 (ttp80) REVERT: C 892 ARG cc_start: 0.8499 (ttt180) cc_final: 0.8158 (ttt90) REVERT: C 1067 ARG cc_start: 0.8229 (ttp80) cc_final: 0.7993 (ttt90) REVERT: D 113 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8140 (ttp80) REVERT: D 171 ARG cc_start: 0.7363 (ttm170) cc_final: 0.7130 (ttp80) REVERT: D 259 GLN cc_start: 0.6818 (mm110) cc_final: 0.6379 (mt0) REVERT: D 315 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7199 (tm) REVERT: D 316 GLU cc_start: 0.8077 (mp0) cc_final: 0.7812 (mp0) REVERT: D 430 MET cc_start: 0.8153 (mmm) cc_final: 0.7924 (mmt) REVERT: D 509 MET cc_start: 0.6756 (ttt) cc_final: 0.5809 (mmp) REVERT: D 577 TYR cc_start: 0.9036 (t80) cc_final: 0.8819 (t80) REVERT: D 594 LEU cc_start: 0.9571 (tp) cc_final: 0.9311 (tp) REVERT: D 601 ARG cc_start: 0.8490 (mtp-110) cc_final: 0.8183 (ptm160) REVERT: D 629 GLU cc_start: 0.8754 (tt0) cc_final: 0.8181 (tt0) REVERT: D 804 ASP cc_start: 0.7271 (t0) cc_final: 0.6805 (t0) REVERT: D 1029 LEU cc_start: 0.9502 (tp) cc_final: 0.9095 (tp) REVERT: D 1067 ARG cc_start: 0.8230 (ttp80) cc_final: 0.8014 (ttt90) REVERT: D 1116 GLU cc_start: 0.7776 (pp20) cc_final: 0.7485 (tm-30) REVERT: D 1129 LYS cc_start: 0.8942 (ttpt) cc_final: 0.8046 (ptmt) outliers start: 134 outliers final: 106 residues processed: 890 average time/residue: 0.1970 time to fit residues: 279.5527 Evaluate side-chains 878 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 763 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1059 LYS Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 570 ASN Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 656 GLN Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1154 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 183 optimal weight: 0.1980 chunk 163 optimal weight: 0.9990 chunk 226 optimal weight: 0.9980 chunk 54 optimal weight: 0.0270 chunk 125 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 chunk 295 optimal weight: 0.7980 chunk 201 optimal weight: 0.9990 chunk 303 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 786 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 ASN B 656 GLN B1070 HIS ** B1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 ASN C 570 ASN C 656 GLN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN D 656 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.179594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.131143 restraints weight = 47285.630| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.69 r_work: 0.3378 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30824 Z= 0.134 Angle : 0.695 13.634 41844 Z= 0.333 Chirality : 0.041 0.297 4716 Planarity : 0.005 0.065 5252 Dihedral : 6.191 58.238 5002 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % Rotamer: Outliers : 4.47 % Allowed : 24.55 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.14), residues: 3728 helix: 1.05 (0.11), residues: 2352 sheet: -3.41 (0.33), residues: 192 loop : -2.57 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1064 TYR 0.019 0.001 TYR D 256 PHE 0.037 0.001 PHE B 578 TRP 0.020 0.002 TRP D 133 HIS 0.014 0.001 HIS D 447 Details of bonding type rmsd covalent geometry : bond 0.00308 (30820) covalent geometry : angle 0.69525 (41836) SS BOND : bond 0.00030 ( 4) SS BOND : angle 0.39302 ( 8) hydrogen bonds : bond 0.03597 ( 1510) hydrogen bonds : angle 4.16280 ( 4470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 787 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7659 (mpt) cc_final: 0.7340 (mpt) REVERT: A 254 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7620 (mt-10) REVERT: A 260 GLN cc_start: 0.7807 (mm110) cc_final: 0.7570 (mm110) REVERT: A 364 TYR cc_start: 0.7042 (t80) cc_final: 0.6592 (t80) REVERT: A 410 GLN cc_start: 0.9293 (mt0) cc_final: 0.8994 (tp-100) REVERT: A 430 MET cc_start: 0.8052 (mmm) cc_final: 0.7740 (tpp) REVERT: A 431 ASP cc_start: 0.9022 (m-30) cc_final: 0.8802 (m-30) REVERT: A 629 GLU cc_start: 0.8848 (tt0) cc_final: 0.8472 (tt0) REVERT: A 656 GLN cc_start: 0.8768 (mt0) cc_final: 0.8120 (mp10) REVERT: A 660 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8738 (mp10) REVERT: A 776 TRP cc_start: 0.8462 (m100) cc_final: 0.8215 (m100) REVERT: A 804 ASP cc_start: 0.7426 (t0) cc_final: 0.6971 (t0) REVERT: A 827 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7696 (tp30) REVERT: A 857 ARG cc_start: 0.7097 (ttm110) cc_final: 0.6663 (ptp-110) REVERT: A 892 ARG cc_start: 0.8616 (ttt90) cc_final: 0.8359 (ttt90) REVERT: A 907 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9360 (mt) REVERT: A 910 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8775 (m-80) REVERT: A 952 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8843 (pt) REVERT: A 1029 LEU cc_start: 0.9544 (tp) cc_final: 0.9168 (tp) REVERT: A 1067 ARG cc_start: 0.8225 (tmm-80) cc_final: 0.7912 (ttt90) REVERT: A 1116 GLU cc_start: 0.7667 (pp20) cc_final: 0.7379 (tm-30) REVERT: A 1160 LYS cc_start: 0.8978 (pttp) cc_final: 0.8578 (pptt) REVERT: B 186 MET cc_start: 0.8192 (mpt) cc_final: 0.7873 (mpt) REVERT: B 249 PHE cc_start: 0.8171 (t80) cc_final: 0.7927 (t80) REVERT: B 397 LEU cc_start: 0.9241 (tt) cc_final: 0.9013 (tp) REVERT: B 430 MET cc_start: 0.8040 (mmm) cc_final: 0.7420 (tpt) REVERT: B 509 MET cc_start: 0.6613 (ttt) cc_final: 0.5636 (mmp) REVERT: B 615 LEU cc_start: 0.9307 (tp) cc_final: 0.9038 (tp) REVERT: B 629 GLU cc_start: 0.8775 (tt0) cc_final: 0.8293 (tt0) REVERT: B 786 ASN cc_start: 0.8515 (m-40) cc_final: 0.8276 (m-40) REVERT: B 804 ASP cc_start: 0.7254 (t0) cc_final: 0.6770 (t0) REVERT: B 828 GLU cc_start: 0.8276 (tp30) cc_final: 0.7997 (tp30) REVERT: B 855 ARG cc_start: 0.7936 (ptp-170) cc_final: 0.7714 (ptp-170) REVERT: B 857 ARG cc_start: 0.7029 (ttm110) cc_final: 0.6672 (ptp-110) REVERT: B 859 TYR cc_start: 0.8440 (t80) cc_final: 0.8185 (t80) REVERT: B 952 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9019 (pt) REVERT: B 1059 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.8024 (mmtp) REVERT: B 1067 ARG cc_start: 0.8274 (tmm-80) cc_final: 0.7966 (ttt90) REVERT: B 1116 GLU cc_start: 0.7814 (pp20) cc_final: 0.7530 (tm-30) REVERT: C 249 PHE cc_start: 0.8222 (t80) cc_final: 0.7928 (t80) REVERT: C 315 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7256 (tm) REVERT: C 355 MET cc_start: 0.5089 (mmm) cc_final: 0.4823 (mmt) REVERT: C 397 LEU cc_start: 0.9241 (tt) cc_final: 0.8980 (pp) REVERT: C 509 MET cc_start: 0.6703 (ttt) cc_final: 0.5669 (mmp) REVERT: C 576 MET cc_start: 0.8747 (tpp) cc_final: 0.8538 (tpp) REVERT: C 607 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: C 611 ARG cc_start: 0.8675 (ttm110) cc_final: 0.8419 (ttp80) REVERT: C 629 GLU cc_start: 0.8704 (tt0) cc_final: 0.8266 (tt0) REVERT: C 776 TRP cc_start: 0.8260 (m100) cc_final: 0.8016 (m100) REVERT: C 827 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7595 (tp30) REVERT: C 857 ARG cc_start: 0.6812 (ttm110) cc_final: 0.6320 (ptp-110) REVERT: C 882 ARG cc_start: 0.8822 (ttp80) cc_final: 0.8606 (ttp80) REVERT: C 892 ARG cc_start: 0.8456 (ttt180) cc_final: 0.8144 (ttt90) REVERT: D 113 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8209 (ttp80) REVERT: D 259 GLN cc_start: 0.6727 (mm110) cc_final: 0.6378 (mt0) REVERT: D 315 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7139 (tm) REVERT: D 316 GLU cc_start: 0.8106 (mp0) cc_final: 0.7849 (mp0) REVERT: D 509 MET cc_start: 0.6819 (ttt) cc_final: 0.5885 (mmp) REVERT: D 580 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8841 (mt-10) REVERT: D 594 LEU cc_start: 0.9559 (tp) cc_final: 0.9299 (tp) REVERT: D 629 GLU cc_start: 0.8798 (tt0) cc_final: 0.8300 (tt0) REVERT: D 804 ASP cc_start: 0.7258 (t0) cc_final: 0.6799 (t0) REVERT: D 1029 LEU cc_start: 0.9490 (tp) cc_final: 0.9084 (tp) REVERT: D 1116 GLU cc_start: 0.7693 (pp20) cc_final: 0.7475 (tm-30) REVERT: D 1129 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8049 (ptmt) outliers start: 138 outliers final: 113 residues processed: 870 average time/residue: 0.1952 time to fit residues: 271.7316 Evaluate side-chains 876 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 753 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 570 ASN Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 910 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 570 ASN Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1059 LYS Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 656 GLN Chi-restraints excluded: chain C residue 657 LEU Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1121 LEU Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 656 GLN Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1127 VAL Chi-restraints excluded: chain D residue 1154 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 312 optimal weight: 0.8980 chunk 180 optimal weight: 0.0370 chunk 143 optimal weight: 4.9990 chunk 287 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 373 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 318 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 283 optimal weight: 7.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 584 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 350 GLN B 570 ASN B 573 GLN B 656 GLN B 831 GLN B1070 HIS B1108 HIS C 404 ASN C 570 ASN C 573 GLN ** C 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 ASN D 656 GLN ** D 786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.179544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131808 restraints weight = 47088.941| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.86 r_work: 0.3370 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30824 Z= 0.136 Angle : 0.712 13.404 41844 Z= 0.343 Chirality : 0.042 0.295 4716 Planarity : 0.005 0.074 5252 Dihedral : 6.169 58.045 5002 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.73 % Favored : 92.17 % Rotamer: Outliers : 4.05 % Allowed : 25.00 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.14), residues: 3728 helix: 1.05 (0.11), residues: 2348 sheet: -3.37 (0.33), residues: 192 loop : -2.56 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1064 TYR 0.026 0.001 TYR C 364 PHE 0.039 0.001 PHE B 578 TRP 0.025 0.002 TRP C 403 HIS 0.013 0.001 HIS D 447 Details of bonding type rmsd covalent geometry : bond 0.00315 (30820) covalent geometry : angle 0.71172 (41836) SS BOND : bond 0.00027 ( 4) SS BOND : angle 0.35488 ( 8) hydrogen bonds : bond 0.03623 ( 1510) hydrogen bonds : angle 4.21790 ( 4470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7456 Ramachandran restraints generated. 3728 Oldfield, 0 Emsley, 3728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 771 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7657 (mpt) cc_final: 0.7367 (mpt) REVERT: A 254 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7570 (mt-10) REVERT: A 260 GLN cc_start: 0.7837 (mm110) cc_final: 0.7576 (mm110) REVERT: A 364 TYR cc_start: 0.7080 (t80) cc_final: 0.6627 (t80) REVERT: A 410 GLN cc_start: 0.9289 (mt0) cc_final: 0.8993 (tp-100) REVERT: A 430 MET cc_start: 0.8057 (mmm) cc_final: 0.7669 (tpp) REVERT: A 629 GLU cc_start: 0.8882 (tt0) cc_final: 0.8513 (tt0) REVERT: A 660 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8733 (mp10) REVERT: A 776 TRP cc_start: 0.8303 (m100) cc_final: 0.7604 (m100) REVERT: A 827 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7741 (tp30) REVERT: A 857 ARG cc_start: 0.7179 (ttm110) cc_final: 0.6773 (ptp-110) REVERT: A 892 ARG cc_start: 0.8583 (ttt90) cc_final: 0.8354 (ttt90) REVERT: A 910 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8771 (m-80) REVERT: A 952 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8844 (pt) REVERT: A 1029 LEU cc_start: 0.9550 (tp) cc_final: 0.9144 (tp) REVERT: A 1067 ARG cc_start: 0.8202 (tmm-80) cc_final: 0.7900 (ttt90) REVERT: A 1116 GLU cc_start: 0.7586 (pp20) cc_final: 0.7309 (tm-30) REVERT: A 1160 LYS cc_start: 0.8969 (pttp) cc_final: 0.8577 (pptt) REVERT: B 186 MET cc_start: 0.8156 (mpt) cc_final: 0.7910 (mpt) REVERT: B 249 PHE cc_start: 0.8172 (t80) cc_final: 0.7916 (t80) REVERT: B 289 GLU cc_start: 0.5974 (tp30) cc_final: 0.5709 (tp30) REVERT: B 430 MET cc_start: 0.8056 (mmm) cc_final: 0.7476 (tpt) REVERT: B 509 MET cc_start: 0.6628 (ttt) cc_final: 0.5655 (mmp) REVERT: B 629 GLU cc_start: 0.8804 (tt0) cc_final: 0.8340 (tt0) REVERT: B 804 ASP cc_start: 0.7248 (t0) cc_final: 0.6759 (t0) REVERT: B 828 GLU cc_start: 0.8376 (tp30) cc_final: 0.8138 (tp30) REVERT: B 855 ARG cc_start: 0.7925 (ptp-170) cc_final: 0.7706 (ptp-170) REVERT: B 857 ARG cc_start: 0.7015 (ttm110) cc_final: 0.6665 (ptp-110) REVERT: B 859 TYR cc_start: 0.8440 (t80) cc_final: 0.8209 (t80) REVERT: B 952 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9017 (pt) REVERT: B 1067 ARG cc_start: 0.8299 (tmm-80) cc_final: 0.7913 (ttt90) REVERT: B 1116 GLU cc_start: 0.7770 (pp20) cc_final: 0.7493 (tm-30) REVERT: C 249 PHE cc_start: 0.8229 (t80) cc_final: 0.7942 (t80) REVERT: C 289 GLU cc_start: 0.5552 (tp30) cc_final: 0.4980 (tp30) REVERT: C 315 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7266 (tm) REVERT: C 364 TYR cc_start: 0.6779 (t80) cc_final: 0.6464 (t80) REVERT: C 397 LEU cc_start: 0.9252 (tt) cc_final: 0.8988 (tp) REVERT: C 509 MET cc_start: 0.6698 (ttt) cc_final: 0.5668 (mmp) REVERT: C 629 GLU cc_start: 0.8737 (tt0) cc_final: 0.8312 (tt0) REVERT: C 776 TRP cc_start: 0.8229 (m100) cc_final: 0.7971 (m100) REVERT: C 857 ARG cc_start: 0.6859 (ttm110) cc_final: 0.6350 (ptp-110) REVERT: C 882 ARG cc_start: 0.8830 (ttp80) cc_final: 0.8612 (ttp80) REVERT: C 892 ARG cc_start: 0.8487 (ttt180) cc_final: 0.8192 (ttt90) REVERT: D 113 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8187 (ttp80) REVERT: D 259 GLN cc_start: 0.6657 (mm110) cc_final: 0.6354 (mt0) REVERT: D 315 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7187 (tm) REVERT: D 316 GLU cc_start: 0.8041 (mp0) cc_final: 0.7798 (mp0) REVERT: D 405 ARG cc_start: 0.7706 (mtp85) cc_final: 0.7437 (mtp85) REVERT: D 509 MET cc_start: 0.6737 (ttt) cc_final: 0.5837 (mmp) REVERT: D 594 LEU cc_start: 0.9549 (tp) cc_final: 0.9285 (tp) REVERT: D 629 GLU cc_start: 0.8844 (tt0) cc_final: 0.8476 (tt0) REVERT: D 776 TRP cc_start: 0.8413 (m100) cc_final: 0.7765 (m100) REVERT: D 804 ASP cc_start: 0.7228 (t0) cc_final: 0.6761 (t0) REVERT: D 857 ARG cc_start: 0.6890 (ttm110) cc_final: 0.6425 (ptp-110) outliers start: 125 outliers final: 108 residues processed: 847 average time/residue: 0.1909 time to fit residues: 261.3468 Evaluate side-chains 867 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 752 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 874 CYS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain A residue 910 PHE Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1002 HIS Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1165 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 377 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 656 GLN Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 869 LEU Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 874 CYS Chi-restraints excluded: chain B residue 907 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 939 VAL Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1038 LEU Chi-restraints excluded: chain B residue 1070 HIS Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1125 GLU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 404 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 570 ASN Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 702 LEU Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 867 CYS Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 874 CYS Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1023 LEU Chi-restraints excluded: chain C residue 1038 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain C residue 1121 LEU Chi-restraints excluded: chain C residue 1159 LEU Chi-restraints excluded: chain C residue 1165 ILE Chi-restraints excluded: chain D residue 113 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 404 ASN Chi-restraints excluded: chain D residue 445 ILE Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 656 GLN Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 874 CYS Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 952 LEU Chi-restraints excluded: chain D residue 1038 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1081 VAL Chi-restraints excluded: chain D residue 1127 VAL Chi-restraints excluded: chain D residue 1154 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 164 optimal weight: 0.5980 chunk 301 optimal weight: 8.9990 chunk 219 optimal weight: 9.9990 chunk 259 optimal weight: 1.9990 chunk 204 optimal weight: 0.0060 chunk 358 optimal weight: 0.3980 chunk 197 optimal weight: 8.9990 chunk 281 optimal weight: 0.9990 chunk 298 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN A 570 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 570 ASN B 656 GLN B 831 GLN B1070 HIS ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 GLN C 404 ASN C 570 ASN C 656 GLN ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS D 404 ASN D 424 HIS D 573 GLN D 656 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.178864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130361 restraints weight = 47547.009| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.72 r_work: 0.3368 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30824 Z= 0.148 Angle : 0.723 13.164 41844 Z= 0.348 Chirality : 0.042 0.297 4716 Planarity : 0.005 0.071 5252 Dihedral : 6.159 59.224 5001 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.91 % Favored : 91.98 % Rotamer: Outliers : 4.15 % Allowed : 25.42 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.14), residues: 3728 helix: 1.05 (0.11), residues: 2348 sheet: -3.33 (0.33), residues: 192 loop : -2.52 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1064 TYR 0.026 0.002 TYR B 364 PHE 0.042 0.001 PHE B 578 TRP 0.021 0.002 TRP D 133 HIS 0.012 0.001 HIS D 447 Details of bonding type rmsd covalent geometry : bond 0.00345 (30820) covalent geometry : angle 0.72327 (41836) SS BOND : bond 0.00020 ( 4) SS BOND : angle 0.45842 ( 8) hydrogen bonds : bond 0.03710 ( 1510) hydrogen bonds : angle 4.26686 ( 4470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9582.54 seconds wall clock time: 163 minutes 54.45 seconds (9834.45 seconds total)